To answer the op, lots of reasons.
One I haven't seen stated in this thread yet is; it's hard to even keep your hands up in boxing all the time. It takes a great deal of training to obtain the endurance to keep your hands high for even a round, let's alone as fight. The higher the hands the more it taxes the endurance of shoulders and upper arms. As you take damage, it becomes even more difficult. Being punched in the shoulders, arms makes it much harder (Canelo, for example, purposely aims for upper arms and shoulders for this reason). Being punch in the body interrupts breathing, which reduces o2 intake, which effects endurance, which makes its harder to keep your hands high etc etc. Keeping a high guard is an aerobic activity. A pretty hard one in fact.
MMA fighters have two additional major factors that exasperate the difficulty
1 - MMA fighters are not training striking as often as boxers/Mt fighters. They have to devote training days to the other parts of mma. Its like wondering why a marathon runner is better at marathons than a triathlete.
2 - grappling wears out the upper arms and shoulders fast while draining the fighters gastank at an accelerated rate. Think of GSPs tactic in his 2nd fight with Penn, "Filling the shoulders with blood." Same idea but applied to keeping hands up.
Long story short, it's really hard to keep your hands up round after round in mma and MMA fighters are blessed thier gloves only weigh 4oz instead of 8 or 10, which would make it even harder to keep hands up.
For anyone who is a fan (which is totally cool and in no way a judgement from me) and hasn't trained. Put your back against a wall, hold things in your hands that are between 4 and 16ozs then try and maintain a high guard for 5 minutes. You'll get it then.
I'll leave the other parts to other posters. TDD, range awareness (big reason), lack of skill, smaller gloves etc.