Of course hydraulic brakes would perform better than mechanical in a static head-to-head comparison, but that's not your problem. It sounds to me like you have had a sudden drop in performance compared to a previous period on the same set of brakes. I have mechanical disk brakes and I've never noticed a drop off in performance. ( I don't really maintain them either, to be honest.)
My original conclusion still stands: Since you've eliminated the cleaner and I'm going to assumeme the surface area is the same, I would put it down to pad material and break-in. Clean the old pads REALLY well with automotive brake cleaner, and re-install them. If you really can't get them clean, then try burnishing the rotors and bedding the new pads to them as I described above.
If you didn't have any problems with the performance of your mech. disks prior to this problem, then I woulden't bother going up to hydraulic unless your doing some serious DH or something. They're not cheap, they're harder to maintain, and they get brake fade if they get too hot. (Then you'll really have a problem stopping, lol)