I think this thread needs its name changing.
I'll voice my thoughts anyway.
The vast majority of games only need one region. RB, RS, DP and BW all have one region, and people like them just fine. GS has two regions, but Kanto is very much tacked-on and is on par with other games' post-E4 content rather than being "the second half of the adventure".
No, seriously, one region. Your masterpiece is probably too long and convoluted, and would be a better game if you had the sensibility to boil it down. It also means it's less work to do, which means a higher chance of it being completed. Only very exceptional games can be long enough to consider the existence of the level cap (which is just one of the many related issues). Swallow your pride - your game is probably not one of these exceptions.
My main concern, which people never seem to address, is what they would actually do with their multiple regions and how they'd seamlessly link them together. If the only reason the player is jetting off to Hoenn is "because Prof. Oak suggested it", then you should throw away anything you've written after that point - it's not part of the same game. Nostalgia cruise games inevitably involve recreating the official games almost word for word (i.e. start off in the starting towns, with/without your previous Pokémon, progress in the same way through the regions, blah blah blah). No. Bad. And don't come to me saying you have some twists planned - deep down you know why you added the extra region, and if that reason is "I wanted it, and I'll find a way to work it in somehow" then that's a bad reason and you should feel bad. You should do what the game needs, and it
never needs someone throwing in extra regions for nostalgia's sake.
If you're particularly stubborn and still want your 5(/6/7/8) regions in your game, then you'll need to start thinking about that level cap and the related issues (level-up move-learning, evolutions, power escalation, etc.). There have been several proposals in this thread on how to fix this, and they're all rubbish. Raising the level cap just results in unrealistically-levelled wild Pokémon roaming Unova (and involves way too much balancing issues for your liking); halving the Exp gain per battle just makes it twice as hard to level up at the beginning of the game (which is off-putting, and still has balancing issues); and starting a new region afresh with no old Pokémon is the same thing as starting a brand new different game (in which case, make them different games, duh).
The official games match the Pokémon growth (fairly) well to their pace. By the end of the game your Pokémon have grown into pretty much their final form with their final moveset (levelling them up to the cap is academic when nothing else about them is going to change). Some are easier to get to that state, some are harder. The point is that Pokémon and the game both reach the end at around the same point. Adding multiple regions suddenly doubles the length of the plot, while the Pokémon are still geared around a 1-region growth rate. This is why the aforementioned level cap and related issues exist.
I've been assuming here that there is no such thing as post-game in these fangames, and with good reason. Aside from a few side-quests, the only thing you can do in official games post-game is battle other players and try to complete the local Battle Frontier. These are negated by the fact that PvP isn't available in Essentials, and very few people are going to bother trying to get bragging rights in a fangame's knock-offs of the official games' Frontiers, because to do so is pointless. This just leaves the side-quests, which can either be shifted earlier in the game or left there to do nothing but be the "for completeness" part. Either way, once the main game is finished, there's nothing left to play for. Therefore, no post-game.
Here are some random ideas I've had about using multiple regions. Their usabilities may vary; I'm just mentioning them regardless of how well they would actually work.
- All regions don't need to be the same size. Those islands in FRLG were smaller than Kanto, for instance (well, they felt smaller).
- You don't need to be able to visit all parts of a given region. This is of particular interest to those who want to use those regions in their plots rather than just including them for nostalgia cruises. I don't think any plot where you suddenly hop to a new region could cope with having that entire region thrown into it.
- You could move back and forth between regions at will, rather than be stuck in a strict linear progression. Puzzles and plot could jump around between the regions. Regions separated by large distances may have some fridge logic to answer to (particularly if the plot becomes ostensibly time-urgent), and people may question why you need two regions when you could use one.
- You don't need to play through the regions in the same way the official games do. GS is an example of this, where you start off in Kanto in Vermillion City rather than Pallet Town, and head off in way different directions.
- Regions don't need to depict different areas in the same world. How about different layers of existence (world/Shadow Realm/Aether), or parallel realities, or different time periods of the same location?