The Ninja 250 is an awesome starter bike.
If the bike has been rejetted with the pipe modifications, its worth it, adding aftermarket pipes can affect the leaner jetting that these bikes come with (even leaner in CA market).
As for tires, I hate race take off's they are cheap but they dont last. They are sold after a few heat cycles but in generally they are great for hard riding, but they will wear out fast. I prefer the Bridgestone Battleaxe BT45 series (if they got it for your wheels). I use BT 45 SpecH for my 2001 GS500.
The Ninja 250 stock shock IMHO is a peice of crap, so anything better than the 250 stock shock. Chances its got a Olhin's shock in the back. You might want to consider progressive springs up front for later on.
As for pasttic replacement and stuff, its expensive for any bike, not just the 250 ninja.
I woudl say get the bike.. its a sweet bike. Yes the power comes on suddenly, but i guess some ppl havent ridden higher powered bikes. Even my GS500 power comes on suddenly after 7K. The only thing you got to remember about hte baby 250 is that its power kicks in after 9K.
Take the MSF course and invest in some good gear.