For veteran players, this is no surprise. But for all of the new players joining, here are (most) of the things I learned after beating Unova. Some of these things might apply to the Kanto and Hoenn playthroughs, but if/when I do those I'll make an extra set of notes.
My team I used for the Elite 4,
Ivy - Serperior lvl 50
Leaf Blade | Aqua Tail
Leech Seed | Coil
Silk - Liepard lvl 50
Night Slash | Fake Out
Assist | Shadow Claw
Charlie - Gigalith lvl 52
Rock Slide | Iron Defense
Bulldoze | Stealth Rock
Ross - Electross lvl 50
Volt Switch | Flash Cannon
Charge Beam | Thunder Wave
Blaziken lvl 53
Brick Break | Blaze Kick
Mirror Move | Acrobatics
Paradaxe - Haxorus (My max attack and speed IV and EV trained monster) lvl 52
Dragon Claw | Dig
False Swipe | Dragon Dance
Now time for some complaints I see everywhere...
"Ugh... why is this game so hard?!?!"
The default answer is "The devs like it hard , so it be like it do", and while that is partly true, the real reason is that adding cooperative multiplayer elements to anything makes it easier. To counteract this, some elements have to have added costs or be restricted. If I want to make the 3DS games beatable in an hour, all I have to do is wonder trade or dig into the PokeBank until I get something useful, and power through the gyms and trainers until I get enough badges/stamps. While the main series games do have multiplayer capabilities, they are most definitely made as a single player game. Knowing the ebb and flow of a MMO is just as important as knowing the the region you are going into.
Though I will say without external help, the first few gyms are rough in Unova. If you forego trading like I did until Nimbasa, losing a few battles and grinding is the only way you going to get through this. Granted, I picked the hardest starter (Snivy) and decided to make it even harder by not picking up Panpour. I had Oshawott in an alt account I used to trade my Boldore to evolve it, so I traded myself a Venipede and that really makes Cheren and Cillian a breeze. Wayyy better than Pansear. When you get the fourth badge, the world opens up and it does get better. I did a lot grinding in the beginning and right before the Elite 4, but with steady progress it took a little under 40 hours. If you want to beat the game in a few hours, good luck.
Something you might have heard is that the shiny rate is really, really low. Like 1 in ~30,000 low. I can't verify this is still implemented, but it's another case of how multiplayer changes things. I personally would have shinies a little more common so they would cost a few hundred thousand dollars in-game instead of the millions they go for, but that's just me. Not that they cannot be found, but if you really want a specific shiny it's actually easier to get the in-game money needed to buy it from someone else.
"Trading would be great, but what about those level caps. And they apply to my pokemon too!"
First, let me put up the chart for badge obedience (also this information might be inaccurate but this tweet is the only place I've found for all three regions) Thanks for the updated info, Akshit! Also, traded pokemon beyond the cap will always refuse to obey at all, while owned and traded pokemon under the cap can't level up past the cap.
Badges Kanto Hoenn Unova
0 20 20 20
1 26 24 24
2 32 28 27
3 37 33 31
4 46 35 35
5 47 38 38
6 50 44 42
7 55 47 45
8 62 58 56
Elite 4 100 100 100
Now that's out of the way, reason one for this change up is the whole "multiplayer makes things easier" thing. The second reason is to curb players from just over-leveling one or two pokemon. This is an acceptable habit in single player but in an environment that encourages multiplayer interactions, over-leveling you main pokemon is a noob trap. Even in the early game this can make a difference. Without this, early game matches would essentially be the team leader vs team leader aka a really lame monotype team since every other team member is filler. While annoying at times, especially when you have that one team member who evolves at a level or two past the cap (I'm looking at you, Tynamo) it helps nudge players to make better teams.
The fact that pokemon can't go beyond the level cap did help me be okay with putting traded pokemon on my team, ironically. I mean, in most of the main series games I avoided using traded pokemon because they would level past their cap and become a liability. With the cap, traded pokemon in Pokemmo are as obedient as your pokemon but they get a boost in experience. Win-win!
"Everything... cost... MONEY!"
Yep, that's the mmo part of Pokemmo. Finding a shiny is almost like winning the lottery because its a super rare thing that can give you millions of dollars, but good luck getting fast money elsewhere. The good news is that Pokemmo opens more pathways to renewable sources of income than the single player counter parts, such as being able to rematch gym leaders, and being able to sell pokemon through the Global Trade Link. The GTL doesn't open up to you until after you get your fourth badge, but selling off high IV pokemon you caught along the way is a great way to make fast cash.
I was surprised that TMs are single use, even in Unova. Again, it makes sense from a mmo standpoint to have a money sink, but thankfully almost all TMs are sold at marts. If you know your needed TM is found in the wild, this might be an incentive to go and find it. Also there is the breeding costs, but let's give breeding its own topic.
"Umm yeah, what's up with breeding? Why can I only get one egg?"
It was a shock that you lose the parents (and held items) in breeding and only an egg is given to you. The one egg thing is mostly to prevent over saturation of certain pokemon, that would decrease their value. If you need an example, look at wonder trade. If I ever needed a competitive Charizard, I could wonder trade a box of zigzagoon for a 5-6 IV Charmander with egg moves and everything. It's also a check to make sure that pokemon that could only be once, those only obtainable in the post game, or otherwise difficult to find aren't just farmed. That said, a lot of gift pokemon can be found in the wild, because otherwise every one-time gift pokemon would equal one save file, since no new members of a species could be created. In a probably-not-intended kind of way, this breeding system means that no family member can breed with another.
I really only used breeding for my Haxorus, but If anyone has a link to the altered breeding mechanics I'll update this post to include it.
"Wait... where's X? I can't find it on the GTL?"
Pokemmo is still adding new features and pokemon, but yours may not be implemented yet. Technically, Zoroark and Zorua are in the game but at the time of writing this their abilities do nothing. This doesn't hinder them from being on N's team (and I'm really glad he has one in all of his teams), but these pokemon will need some more fine-tuning before being released to the masses. I'll be thrilled when it gets released, but for now I'll just bide my time.
Also some pokemon are intentionally unavailable to begin with. All legendaries excluding Mewtwo, Rayquaza, and Zekrom are no where to be found, and even these have special conditions. Should you find Mewtwo or Rayquaza in the Cerulean Cave or Sky Pillar respectfully, then congratulations, you found the only one of its kind in the whole game. If you catch it, your name and location are broadcasted across the region. They release themselves if you log out or put them in the PC. And you can no longer refuse challenges to battle from other players. If you lose, the legendary will go to the victor, so good luck with that. Zekrom's a little different since it's a main part of the story, but you can only use it in the fight against N and Ghetsis. Outside of that, Zekrom stays in your room in Unova. Sorry, Reshiram fans.
"So what's so good about PokeMMO?"
It's really nice to see the pokemon world lived in. Having the restriction on Mewtwo and Rayquaza for example makes these pokemon feel like the elusive, powerful legendaries they are. My main draw to Pokemmo was the 5th gen walking pokemon mod. I had plans on replaying Black and White anyway, but this added a little extra kick. For all that it takes away, Pokemmo adds a lot to the table with newer features, such as player customization, walking pokemon (pokemon gen 1-4 already use their walking sprites from HGSS, but you will need this mod for gen 5), Ability capsules (called ability pills), HM flutes, and other things. If you wanted to add a twist to Kanto, Hoenn, or Unova, this is a great place to start.
tldr; Don't hinder yourself by ignoring the mmo part of Pokemmo, go forth and trade with people. If you're feeling good today, go trade something nice with the people a few badges below you. Just take your time and have fun!