We had two pokémon games in the two past year (or 4games depending on the way you look at it). X/Y in fall 2013 and AS/OR in fall 2014. So it is not too to think that nintendo is aiming to make the franchise yearly and that we will see yet a again a new pokémon game this fall. 

Pokken Fighters.

Pokken is coming out in July in Japanese arcades, they'll likely follow Namco's plan and release the console version a year or so later, don't expect to see it at E3, a console version that is,

Next year is Pokemon's 20th anniversary, they're probably saving stuff for then.

I don't think so. They announced X&Y and ORAS in January of their years. If they were going to release a game this year it would be too late to announce it.

I doubt we'll see a main series entry till next year. They may be prepping to celebrate Pokemon's 20th anniversary. Anyway, I don't recall E3 ever being the place they reveal Pokemon games. Normally it's on Pokemon Smash (I think that's the name of the show) or leaked from CoroCoro.

I find that hard to happen since they just announced Mystery Dungeon, will likely release Pokkén Fighters on Wii U next year and have 2 eshop games only too.

If it is it better not be a main line 3DS game.

I suspect at most Pokken Fighters, as they already showed MD.

No no no. Seriously no, they better not.

Pokemon generally doesn't get announced at E3 - it's one of those franchises that almost always gets announced in Japan first.

If a new Pokemon game of any sort gets announced at E3, it'll be a spinoff that is designed more for the west. One interesting possibility is Pokemon Snap 2, because Pokemon Snap sold far better in the West than in Japan (over 2 million in North America, another 700,000 in PAL regions, and about 650,000 in Japan), at least according to VGChartz.

A Wii U Pokemon title might also end up being announced at E3, as both Colosseum and XD sold better in America than Japan by a noticeable amount... but I doubt it, because Nintendo would probably want to use it to push the Wii U in Japan most of all. This observation also applies to the slim chance of an MMORPG - if it's happening, it'll probably be announced in Japan.

Personally, I'm not expecting any new Pokemon announcements, just further information on the new Super Mystery Dungeon and possibly the first information on Pokken Tournament outside of Japan. This isn't to say that I don't seriously hope for Pokemon Snap 2... but I don't expect it.

Main series? Probably not.