I wouldn't limit strength or agility--I'd just limit the total bonus to the PL cap. If you have Acrobatics or Athletics at 12, and the active ability is at 10, your total bonus is +20.
I'd actually go further than just dual-stat skills, myself. Falling from a height and need to catch something to save yourself? Roll Acrobatics + Dexterity. Meet another athlete and try to get on their good side through your shared knowledge and appreciation of the sport? Athletics + Presence. Trying to recognize the name of a great circus performer? Acrobatics + Intellect. Need to catch somebody cheating? Athletics + Awareness.
There's another d20 game I'm a big fan of, called 13th Age, that drops the 3.x skill system entirely in favor of what it calls Backgrounds. Instead of a lawyer taking Expertise (Law) and Persuasion and Insight, for example, they'd take a background like "lawyer," and whenever they needed to do something they'd have experience with as a lawyer, they'd add that background to whatever ability check was relevant. I'm very, very tempted to steal the background system for the next time I run an M&M game. The increased versatility would probably make them more expensive than skills, though, and I'm not sure yet how much I'd charge for ranks in backgrounds.