Great fight for both of them. Great, great fight. Hard, brutal fight. Stoppage was "okay" - maybe a little too soon but not a bad stoppage by any means. However, Rios will get absolutely decimated if he fights an elite fighter (Manny/Floyd/etc.) or any fighter who can remotely box (stick/move). Obviously Rios and Floyd won't happen because Rios is Top Rank, but Manny/Rios can and probably will happen. Manny will annihilate Rios if they fight, annihilate. Rios cannot fight backing up at all and has ****-poor defense. Also, if you're honest, you'll see he was close to getting stopped against Alvarado. Prior to hurting Alvarado in the sixth, Rios was throwing punches with nothing behind them; he was exhausted, running on fumes, demoralized, and hurt. If Alvarado didn't get hurt in the sixth, he would've stopped Bam Bam.
The only problem I see with your post is that Rios landed a huge right in the 6th and hurt Mike prior to the end of the round. Brandon took half of the 7th off before starting to throw hard punches. Perhaps he was regaining some strength since he was a bit exhausted. Mike was also beginning to gas. Had Mike followed a more disciplined game plan he would of beat Rios but Mike is not that kind of a fighter, specially vs Rios who can bait you into a brawl. Nevertheless, it was a great fight and I agree that MP or JMM would give Rios a boing lesson.
Rios would stand an ok chance against JMM, I think. At the very least he puts up a better effort than Katsidis. But against Pacquiao he could get horribly ruined. That's providing Pacquiao is anything like what he was against Cotto and Marg.
I don't even think it would matter if Manny had an "off" night. He would MURDER Rios. If Alvarado, who has medium hand speed (AT BEST), was getting off first and able to keep Rios on the outside (for some of the fight), then Manny would have a field day. It would be like Mitt Work for Manny, honestly. Rios would be beat to the punch and Manny wouldn't get pinned on the inside like Alvarado. Manny stops Rios within 8 rounds.