Phnom Penh is a friendly, compact little city whose highlights can be seen comfortably in two days. One of its best features is that it's easy to walk around in, and wherever you look it's pleasant and comparatively orderly.
Siem Reap is a completely characterless town which isn't worth any time at all.... wherever you look, it's a tacky tourist town where tiny guest houses stand shoulder-to-shoulder with some of the most tasteless and gargantuan hotels you are ever likely to encounter outside of Las Vegas. The whole atmosphere is one of a town designed around the visitor, determined to provide you with everything you want (and don't want!), in order to separate you from your money. But, of course, it's the dormitory town for Angkor Wat, and while we managed to cover the highlights of this wonder-of-the-world in two days (at the expense of blistered feet), I have heard many people say that you could well spend five days exploring and not see everything.
By all means, then, you should weight your time in favour of Siem Reap..... but only spend enough time in town to eat and sleep; the rest of the time, get a tuk-tuk or a jeep-and-driver, and head out to where the action is.
Two days in PP and three in Siem Reap would be a good way to divide things. Two full days of touring the Angkor area is a minimum to get to the main sites. My favorite tourist place to go in PP is the national museum, which is in a very cool building. It's also a good warm up for Angkor. My favorite hotel in PP is the Amanjaya. Probably would be four star equivalent. It is a small boutique type hotel in a good location. Great breakfast and very nice and large rooms. You need to book ahead though.
Hope this helps.