i am probably not the best person to ask since i was managing chronic pouchitis while pregnant. mine were definitely more runny toward the end, but that could have been because my antibiotic wasn't really working too well anymore (i was on the same one the entire pregnancy). also, in the first trimester, with the change in hormones, my bowels slowed so much, i was only going once a day. so for me, the last three months were a huge increase in frequency and change in consistency.
if you think you have pouchitis, talk to your doctor about a round of either flagyl or augmentin. those are both safe to take in 3rd trimester. i was on low dose of augmentin the whole time.