I found it much easier to play with the clarinet. The viola has intonation problems and is lighter sounding.
Lighter sounding? The viola can produce an incredible rich, dark sound. I'm hoping you mean it's easy to 'bury' them coz the general register they play in doesn't carry all that well.
As a violist, I find that it's easy for the viola to get buried under the piano. It doesn't help that many editions (if not all) have sections of the viola part transcribed an octave lower from what the clarinet would play, even though the original clarinet part is well withing the viola's range. I'm playing this sonata now (on viola) and I'm trying to do as much as possible in the octave written for the clarinet, since a higher sound is more likely to cut through the piano. As for intonation problems... 
So you're changing what Brahms wrote? I've played the fmin and it's quite possible to adjust balance accordingly, just like playing anything with Viola. Any accompanist has ears to listen (assuming their not deaf), it's a matter of using them!
Aside from balance (which should be a natural skill for all accompanists - or associate artists
), the only general thing I can really think of is tempi. Clarinetists tend to take it a faster than viola players, but that can be discussed between the two of you.
Topic: Brahms' Viola/Clarinet Sonatas