Ok, so I'm not sure if you're aware of this, but this idea is brought up a lot. There are threads all over general project m forums dealing with most of the questions you asked in more detail than I can explain. I highly suggest you go dig up those threads if you want comprehensive answers. I can give you some in short answers.
1. Why was Marth's shield breaker changed back to melee version?
The reason is that the stab really added nothing to marth's game that isn't covered by his aerials and ftilt. Aerial melee shield breaker is much more useful than aerial brawl shield breaker. Grounded melee shield breaker hits opponents on ledge, sends at a weird angle and is much harder to jump over. The aerial momentum from brawl shield breaker is meaningless now, because faster fall speeds mean you can't charge it anyway. Also it is too predictable.
2. Why is Roy just a Marth Clone?
He isn't. The change in sweetspot location, speed, falling speed and knock back angles make them play completely differently. Try playing a marth style spacing game with Roy and you will not kill ever. Try to play a more aggressive roy style game with marth and you will die in no time at all. Simply put, they are very different, if you actually look at the effects of their moves. Also, roy is very competitive in project m, just ask Sethlon.
3. Why are fox and falco the same?
Firstly, this is the marth board. You want to discuss the similarities between species here, you'd best be talking about chain grabs (and even those differ between the two). However, I will answer your question this one time.
Fox and falco play completely differently. Fox kills mostly off the top with up smash or up air. Falco kills off the side with the smash or the bottom with dair. Fox's shine sends opponents downward, falcos sends them upwards. Falco is a glass canon sort of character. Fox is not. If you watch high level foxes and falcos you will see the difference.
If you want to know the difference in detail, ask in the fox / falco boards or (ideally) in the general pm boards. If you ask nicely, I'm sure someone can give you a very detailed answer. The reason falcos shine was restored to melee was because the brawl version was almost completely useless from a competitive viewpoint.
Lastly, something I love bringing up from time to time. Project M has its origins in a hack to try to port melee falco into brawl. I know it's come a long way since then, but I still chuckle inside when people complain about falco or ask that he get some of his brawl moves restored.
Also, sorry for any grammar errors but it's 3:30 am right now. I'll come back after I've had a good sleep to clear up any points that I may have butchered.