Don't know about Shotokan but I've done Muay Thai for a good few years along with MMA on the side, and MT is really awesome. Like others said, it'll toughen you up, drastically increase your fitness level if you keep a good diet and do it regularly, and all in all improve your body - I even found myself being more flexible after a while. When it comes to fighting, MT is as good as it gets, it's an art based on offence mainly rather than defence, but if you decide to spar then your dexterity will improve along with your ability to take a hit.
If you're interested in BJJ, it's a really good martial art to do alongside MT if you're interested in starting up MMA, basically as soon as you go to the ground where MT isn't applicable you can use BJJ, which is also pretty offense based. That said, I've only ever done BJJ when i've done MMA, I haven't actually gone to any individual BJJ lessons or anything.
Sorry I can't give you any info about the Shotokan, it might be worth making a thread on a martial art forum and seeing what they have to say about it?