The only way to satisfy everybody's needs is to base the game on the cartoon series. I mean, you don't have to be Ash, Misty or Brock, just a style like that. This is some of what I think should be in it:
-You can make meet people on the way collecting Pokemon (just like Ash did), and if they wish to join you, they can (or can't depending on who you think is cool and who's a total loser). Who you choose on your journey also affects the outcome of each situation you come across, eg different personality traits, etc like in Animal Crossing.
-If indeed it IS an online game, your friends may be real life people, and you can travel with them on your journey. Thing is, with all the time differences and stuff, it might be a bit hard.
-Pokemon Leagues are held once every six months. You must have enough badges (from the offline game) to get in, though. And all the people who DO are entitled to battle it out, Stadium style, for the title and trophie of Pokemon Champion (at least until the next League).
-I don't want new Pokemon to be added as 'patches' or whatever on the net, cause that would scrap the potential for new GB Pokemon games, and be just too confusing.
-People (NPCs) all over the different lands have special items, bonuses, games, Pokemon, Pokeballs, and mini-quests for you to complete, so you can earn whatever you wished for.
-Police stations are set around the areas so that for example, Team Rocket is up to no good, and you are able to stop their plans, you'll earn a great sum of money as the reward, and of course, a extra special reward from the ever beautiful, super-short skirt wearing Officer Jenny (and her infinite number of look-a-like relatives). As such, Giovanni will put teams on you (James, Jessie and Meowth style). The more you are wanted by Team Rocket, the more stars appear on your 'Team Rocket Hitlist' chart, which indicates the level of importance they place on you to get rid of you quickly.
-Pokemon Centres are in every town and city so you can rejuvinate you Pokemon, get a good nights sleep (Save) or oogle over Nurse Joy's sexy innocence (and her relatives - sorry, got carried away there

.
-Of course, Saving is not only in the Pokemon Center. Making it like that would turn playing the game into a chore. Therefore, you can save anywhere in the game, but even so, going into anyone's house that let's you stay there the night is also another better way to save.
-Battling (the most important aspect of the game) MUST be in real-time, to reflect the action and exhiliration of the cartoon. A microphone should be included so that you can bark orders to your Pokemon on the fly, and they will react/obey accordingly. The microphone can be used online for the same urpose, and to talk to others.
-Your Pokemon will grow and nourish according to the amount of time you spend with it, the amount of battle time you give it, and the amount of rest and relaxation you give it. This will be Tamagochi, and Pokemon Pikachu times infinity.
-Your offline NPC friends will grow closer to you, and as you grow, you may even get girlfriends/boyfriends (Ash and Misty, wink wink).
-Back to the League aspect. New Leagues will be announced via your Pokedex. This opens up new areas of the land for you to explore, battle, and get badges for the next league. Of course, this won't happen until all the current leagues are done, so maybe every year a new area is opened up. This, hopefully, creates a low maintenece online paradise, so that the developers can make other games/levels, etc.
I hope some of these ideas are included in the final product. I will still get this game regardless.