You'd be mad to buy a subway when you can get a Deneb.
The first upgrade should be RAM, get it upto 18Mbytes as soon as possible.
Next upgrade is hard drive, get yourself a nice hard drive and a panel IDE->CF adapter
so you can rapidly transfer files from the PC to the Amiga.
Then perhaps a Kickstart 3.1 chip (or even better a home-made KS3.9).
Then a CPU upgrade, perhaps an A3640 as they are ultra cheap at about £30 or go for something more substantial, one with RAM.
Then you've got the decision : Scandoubler or Gfx card. The Indivision A4000 is good, but so is a PicassoIV gfx card.
I wouldn't bother replacing the battery at all but you could replace it with a coin battery if you like, depending on which motherboard version you have there is a set of pins for connecting such things.