Everything is a tradeoff, if you want the ease of HTML+CSS then be prepared to pay the performance hit, and if you want lighting fast GUIs, be prepared to pay the productivity hit.
We are willing to pay this extra cost for these elements because they are often required to be quickly put together and then iterated on over a long period of time in a very dynamic and changing system. Some elements may be moved from Scaleform into a more native implementation but for the most part it is left to be slowly parsed and inefficiently rendered.
Basically, where we need fast changing interfaces that arent necessarily implemented by high skill programmers then we are going to take a performance hit to get the same level of visuals we could get if we had the time and manpower to approach it better.