You might be thinking of the limitations on ROMs that are based on the Android Open Source Project (AOSP) such as CyanogenMod. The difficulty for these developers is that they don't have access to the source code for some of the device drivers of the EVO, and use only code that is available from the AOSP (as well as home-built modifications and code, of course). These drivers are also closely coupled with HTC's proprietary Sense UI, which was a contributing factor to some of the difficulties.
The big dealbreakers for these have always been WiMax/4G and HDMI output. These have actually seen a lot of development as of late, however. For instance, you can get an alpha/test version of CM7 which supports WiMax now. I personally run this on my EVO and it has been very stable, albeit buggy in a few fairly trivial ways. It's definitely fine for daily use at this point, and I have been using it since it came out without any actual issues. It's also slated as a feature for the final release of CM7.
HDMI is a very different beast, and didn't see as much development from the start because there was seemingly less demand for it. However, a few pictures have been posted by devs recently that seem to indicate that progress might be gaining momentum. One such picture can be found here.
If you flash a custom ROM that is based on an HTC ROM, then these concerns essentially go away. The basic rule of thumb is that any Sense UI ROM will support both WiMax and HDMI out, and any AOSP ROM will not (excepting the recent test versions of CM7).
Also, CyanogenMod doesn't come with Google's applications pre-installed due to licensing issues. They are permitted to distribute a separate package, however, so you just have to flash them separately after you flash the ROM itself. Beyond that, everything else functions as normal, and many additional things become possible with root.