I've been a GM and a player in exclusive roll-over systems like Pathfinder and Homebrewed D20 systems with both exclusive roll-under and combined mechanics. This is my experience, it may not be a perfect answer but hopefully it helps.
First a comparison of the aspects that stand out to me about the two systems as a GM.
Roll-over: I've found that the roll-over mechanic is far easier and quicker to fudge when you're putting something together on the fly. I've also found that each individual roll tends to take longer to work out, there's more math involved in getting to the final result, disorganised players make this much worse.
Roll-under: Tends to take more prepwork and is less intuitive when you're setting up, so it's much harder to work on the fly. Once you have the numbers set it's very quick and simple to run for people who are used to it, when you have a group who are either long time players of dedicated roll-over systems or who play dice pool games like Shadowrun getting them into the roll-under habit can be amazingly hard work.
As a player I found the two mechanics to be much the same, I have a target and I get it or I don't, again roll-over takes longer to work out the result for, if there are a lot of bonuses etc... but not that much longer if I'm well organised.
When it comes to combination systems the first system I ever played extensively was a homebrew D20 system that used both under- and over-rolls and at the time I found it reasonably straight forward. A couple of years ago, having played Pathfinder exclusively for several years in the meantime, I went back to it and was amazed by how confusing it was to get back into the habit of most of the game being on over-rolls but having several of the most important mechanics work on a roll-under basis. I ended up having to give the GM my finished roll numbers and trust he had it together, which didn't always work.
In short I don't find that there's a lot to differentiate the two systems but I do find an exclusive system of either roll-under or roll-over more straightforward. Exclusive systems are simpler playing habits to get into they don't have the added complexity of "what kind of roll is this?", all rolls are on the same footing.