Stretch,
I'll answer your questions as best I can, given the 1999 version of my boat, and the way it was rigged when I purchased it in the winter 2004.
1) Mine is rigged with a 200HP Yamaha 0X66. According to the manual, it weighs in at 463 pounds. The listed weight of the 200HPDI is 475 pounds, versus 583 for the F225. I have absolutely no problems with 200HP on my boat, and would actually prefer the 200HPDI for the reduced weight and I'm assuming lower cost.
Since you are thinking about dual batteries and weight distribution, etc.. one option might be to mount the batteries underneath the console, which would shift around 75 pounds forward and negate some of the extra weight of the F225 if you went that route. You could probably mount the remote oil reservoir in the console as well, for a little more weight savings. Mounting the batteries in the console would open up the aft seats for storage, etc.
If its any consolation, I'm sure there has been several occassions when I've had at least two people (~400 pounds) back between the leaning post and the engine and haven't had any problems with water coming into the boat.
2) Not sure what is 'standard' rigging these days, but my boat came with two marine batteries, one installed in each of the aft cockpit seatbox. There is a Perko battery switch in the starboard seatbox, along with the hydraulic trim tab pump.
3) Bilge access is very good. There is a big hatch directly in front of the motor that provides access. I believe the hatch is 23" x 13". The entire area between the hatch/cockpit floor and the hull is open, so you have plenty of room for 2 bilge pumps. There is also a shelf directly below the hatch that holds the remote oil reservoir and has space for a couple of milk crates if needed. I would guesstimate that the distance between the hatch and the hull is around 2', and its all wide open. Definitely not an issue on this boat.
4) I don't have the exact inside dimensions from the 'ceiling' to the 'floor' of the inside of the electronics cabinet, but I do know that the dimensions of the opening are roughly 9" x 30". Here is a pic of my setup, with a Garmin 182 GPS on the left and a Raymarine DS500 on the right, to give you something to compare with.
5) Can't help you on the stock trim-tabs. Mine came with Insta-Trim BoatLevelers. I have no idea what size they are, but they work well enough.
-- Tom