I remember having this same discussion about this same idea before. Everyone says you'll reach level 100 by the time you get to the 3rd region. I keep asking myself... how? By the time you finish G/S/C or HG/SS up to the point before Red, and before the 2nd E4 battle challenge, your main pokemon party's average level is 58-62 (at least it was for me... I don't spend a whole lot of time grinding). I'd say by the time you reach the very last region, then maybe your pokemon levels will be 100. Of course, it also depends on how many trainers you'll implement in your game, how high the pokemon levels for each trainer will be in each area, gym leader pokemon levels... etc.
EXP needed to go from 99 to 100 for certain Pokemon.
Medium Fast: 29,701
Medium Slow: 32,757
That's just one level, plus leveling erratic Pokemon, or fluctuating Pokemon don't level in an ever increasing EXP needed fashion, for instance, erratic Pokemon from 97-98 need 12,206 EXP to level (compared to 8,118 EXP from 99-100).
EXP, if a problem, won't be the only one for making a Pokemon game with all regions. Besides the sheer size, a decent storyline is needed. What motivates the player, and your protagonist to even travel every region? If people wanted to just play in a certain region, they'd boot up the official game and play there. Think about that. Don't make a lazy storyline like you just go to each region to stop their respective villain organizations... that's just... dumb. If I wanted to stop Team Rocket in Kanto, I'd fire up FR/LG, if I wanted to stop Team Aqua or Magma.. I'd fire up Ruby/Sapphire.
If I wanted to battle every gym leader and champion, I'd go play Black/White 2 and play through the Pokemon World Tournament.
Seriously, I don't think the hardest part would be to get all the sprites, music, sounds, maps, bitmaps... whatever... that's cake, but an original, and decent storyline? Good luck with that one, bub!
That's my take on it anyhow.