And i can pick technically any aftermarket HU that i want? are they all universal sizes?
yes. its either DIN or double DIN. most are DIN, which means you need an install kit for a honda/acura. all it does is have a DIN sized opening for your DIN sized aftermarket radio. it will also have a nice pocket for cd's or whatever else because of the gap. the tabs on the sides of the kit are designed to fit in your stock radio spot.
you can choose ANY aftermarket radio. the aftermarket radio will have 10 or so bare wires coming from the back. all you do is get a wire harness for a honda/acura. this wire harness will have 10 or so wires on one end, all the same color as the wires coming from your aftermarket radio. you connect red to red, green to green, and so on. on the other end of this harness will be the plug that plugs directly into the harness coming out of your dash board (that used to plug into your stock radio).
choose whatever radio you like. its about you. its about what features you like and what looks good to you. pioneer, sony, eclipse, kenwood, and alpine are reputable brands that come to mind.
however, bypassing the amp will require some more work. i havent done it before or else i would help you out with that.