"Is it worth putting the money into one?"
No. A X2 is going to take far more to be a good ski than getting a SJ and doing a fix steer conversion hood. If you want a X2, build a X2. If you want a great flatwater freestyle ski, save yourself the trouble and buy a superjet.
"I mostly ride flatwater freestyle with a little surf when I make it to the beach. What is a good setup for flatwater?"
Drop in a 750/800 to race bouy's, but you don't want to race bouy's... A good flatwater setup is a yamaha motor (a few people make conversion plates to bolt them in w/ the kawi pump), an exhaust and custom hoses to match your new motor, a SJ pump (Kawi pump works, but SJ pumps are easier, more reliable, and have more different parts avail... not sure it's worth the work to make the conversion, but if you want the best...), Nose fill/mod (that's what all the Japs do), possibly tubbies (Tom21 sells a set, but I don't believe the japs are using them), shorten the hull 1-4 inches, AM steering (UMI, accusteer, modded stock), hood mods to keep the water out (X2s like to sink, fast), bilges, ummm... start with that...
"What year or specific things should I be looking for in my first one?"
Any year with a "Squirrel Cage" steering (direct steer on them like to bend), a title and a good deal
"How do they differ from stunting and riding a stand up?"
The motor sits far forward so they are heavy in the nose. The poorly designed bottom makes the water spray infront of you so you constantly feel like you are drowning. The ski falls over sideways at 35+ MPH for no reason even if you are doing everything right. The weight forward makes the pump break free in hard turns (hense the leg dragging). They are harder to get on because you can't reach the bars as easy as a stand up (you have to pull yourself up to them, you can side start but the fuxass hood seal lets tons of water in while you do this), the fixed steer not attached to the hood makes working on them a complete bitch, I still haven't been able to get my craftsmen wrench out from where I dropped in by the head pipe, I am probably going to have to pull the fuel tank to get to it, you have to pull the motor to access your bilges, or anything else you place back there, it sucks. The narrower hull makes it suck to work on the motor, no space, and, it's a complete bitch to make anything larger than a stock part fit into the hull, everything has to be custom, my exhaust for example is a 650 manifold with a SJ chamber, SJ waterbox and a 550 tank because the X2 tank wont fit anymore. There's more...
That's a good start. The moral of the story is don't expect it to be an easy build, expect a lot of custom work, and expect you have a need to keep a tool box nearby at all times. There's no such thing as a bolt on part for a X2, even if it was made for the X2. A X2 makes a good second ski. Buy a SJ, 650sx, SXR, w/e as a 1st/primary ski. Plan on the X2 being a hobby.
If you read that and still want to own a X2, then you are just as F'ed up as the rest of us X2 owners and you will fit right in.
Cheers.