Mass Effect's better, more polished, IMO. VO's for PC is great, Mass Effect 2's conversation moves are especially nice (like pushing a guy out of the window to interupt his boring ramble, for example). Combat system involves more skill than Kotor does, conversation wheel is generally more intuitive than plain old text (even though this may seem wrong to persons that would like that what they say be very clear...)... Anyway, both have their plus sides and downsides. For the Mass Effect downsides: they are not very open to modding, which is a pain in the arse if you want a bug to be fixed (by the way, be sure you recruit Samara BEFORE doing the Shadow broker DLC, for ME 2). Also, the maps are not without their flaws (you may fall out of the map in the collector ship, for instance. But then, this happens in TSL too, so...).
One thing however that makes me prefer ME over KotOR is the addition of COVERS. This is a very neat feature to get.