So far, I have had good luck using "Foreign Audio Search" in HB and just burning them in. I would always have forced subs visible regardless, so I just burn them in.
I agree with the use of mkv's, would love to have that capability. I used them with the infamous Popbox. However, I had to have HDD connected directly to the unit. Wifi streaming was problematic, to put it mildly. I think the advantage of the use of mp4's for the aTV is the lower bitrates and limited codecs it uses, which make streaming work really well. And subtitle support is really an mp4 limitation, not necessarily an aTV limitation. For $99 subtitles is only a mild annoyance for me.
The primary reason I can't use ATV is that it can't do full bitrate BDs, and on a 65" TV with a good film, the difference is noticeable (if subtle) between the raw BD sourced MKV and an ATV3 handbrake conversion.... the limited codec support is another problem (I have quite a few VC1 titles).
On the whole though it's a very good box for the majority of consumers. Subtitles though is a real sticking point.