Hybrid Games

So by now the Consensus here is that you should choose a 3D-Engine. I also suggested that. But there is another Thing to keep in Mind, and Game-Designers don't like this, but it is to some Degree a true Fact: People don't like Genre-Mixes.

Of Course, that depends on how far apart the Genres to be mixed are, but if by Strategy you actually meant building and deytroying Bases and Armies, RTS, then that truly is too different from FPS and Adventure, and this is where it gets messy. You sure have it in your Head as a nice Vision and think it would be great to play, but the Truth is that your Game will ONLY appeal to those Players who actually like to play all three Genres. It is risky enough to mix two Genres, but once you mix three very different ones, the Player might most probably play the one Genre, love it, then get to the other Genre, be like "eh, I can like those Games if they are done well, so whatever", and then get to the third Genre and be like "what? I hate that Genre, and now I am forced to play that to get to the next Part of the Genre I actually like??", and very likely, most likely even, the Player might/will quit at that Point -- ragequit maybe. I think Giants -- Citizen Kabuto is a good Example for this Problem.

Your Game could be very good, but appeal to only a few, a very few People. But... let us be very honest: If you have never made a Game in one of these Genres, which I assume, and now you want to make three Games at once, it will probably end up becoming a Mess.
So yes, if you want to stick with that Idea of three separate Genres, you really should switch to a 3D-Engine. But independent of whether you do that or not, I much rather suggest you bring these three Genres closer together, or People probably won't like it at all. I personally think it doesn't matter and it is not about pleasing People but about making one's own Vision come true... but it would be a Shame if you would spend the next Decade creating a Game which nobody wants to play.

So by now the Consensus here is that you should choose a 3D-Engine. I also suggested that. But there is another Thing to keep in Mind, and Game-Designers don't like this, but it is to some Degree a true Fact: People don't like Genre-Mixes.

@caligarimarte Another game that comes instantly to mind is Brütal Legend. I really enjoyed the game when I first started playing it as it was a third person action brawler type thing with the typical loud random craziness of Jack Black & the cameo from Ozzy was great too as was the main menu design. It was all great for me up until it suddently decided to incorporate RTS stage battles into the game as a sort of mini-game that wasn't really a mini-game as the battles could last ages or end quickly depending on how good you are at RTS games - personally I've never been a fan of game like Command & Conquer, but I persevered with the game for the amusing story-line - if it wasn't for the saving grace of Jack Black I would have dropped the game like a sack of potatoes after the first stage battle thing because I hated those sections & they seemed to come more frequently as the game progressed & got even more chaotic & harder with each one.

I tried Daedalic Entertainment's Blackguards game the other year & end up turning that off after 5 minutes because of the cell battle stuff. There's only been the odd one or two games with strategic battles that I've liked & the only that sticks to mind is an old SNES title called Treasure Hunter G.

Thank you all for your input. Some great things to think about. I realize there are many people who don't like to play certain genres and don't want to scare them off if they reach a portion of the game they don't like. I definitely have some changes I'll need to make to the story to make it flow better.