1. Go with a 6.5" coax speaker for the best results and easy swapout in the future. The 3 ways are gimmicks. The Rockford Fosgates listed above are a good choice but I'd get the coax ones in 6.5". There are many more excellent 6.5" speakers available and I'd go with a name HOME speaker brand for the best sound...Infinity, BostonAccoustics, JBL etc.
2. Depth can be handled with spacers like these:
Metra 82-4300 Speaker Adaptors for Universal 1" Plastic Spacer Rings
3. The first thing to do is remove the existing ones and probe around to see how deep you can go and if there is any obstruction to installing larger speakers. 6.5" is ideal...but the other sizes...5.25" and 4" can also give major improvements with quality brands over the crap that comes pre-installed.
You can re-use the existing wiring easily...so it is simply a matter of figuring out what will fit and the mounting process. Good luck!