15 minutes for a 90min. video? It must be giving you rediculously huge file sizes.
I don't have any experience with streaming MKV's via Xbox/Ps3 etc but I thought there was a way to do it..
However you should also look inside your MKV and see if its a raw h.264. See if your system is capable of playing that back, although since its MKV its likely VFR and that will produce problems trying to play it outside the MKV..
So your best option likely is to convert. But you have to do it properly if its VFR or you'll get choppy playback, etc..
You should try and find out if your Xbox can be setup to playback Divx HD or something, with a firmware hack, etc.. If it supports x264/H264 you can try encoding an AVI with an x264 codec.. Probably get a hell of a lot better file size, etc too, even though it takes longer.. I never sacrifice quality/file size for faster encoding.
If you're lucky, it may be that the fast speeds you get are because the program is TRANScoding instead of encoding. I believe transcoding does minimal to no encoding if the codec you are transcoding to is the same as the source, etc. So if its a matter of switching the container then its likely transcoding or something.. Hard to say without me looking at your specific file and the program you're using.
That GOT-whatever program seems to be doing that.. MP4 is just another container like MKV so its probably demuxing the MKV, and putting the source files and timecodes, etc into an MP4 container.. Basically just remuxing. Which is pretty much the best solution you can use.