Triode seems a little smoother, more liquid. Pentode is a bit bolder, more highs and lows. John Petrucci specifically liked the 60/100w IIC+s because they were Pentode, and it's definitely a little more aggressive and chunky. But I'll still switch between them regularly.
In the Mark V 25/35w you've got more going on because it's also dropping to 2 tubes and significantly reducing the headroom and volume. That change in headroom might be more noticeable than the tone changes and is certainly harder to compare when the volume is jumping. I'll say in most cases for high gain metal power section overdrive can hurt more than help, it can take you big low end and make it feel flubby, it can blur your definition. There is a reason Rectifiers come in 150w and most heads are still 100w when that power isn't really needed for much anymore. Lots of preamp gain with a clean power section seems to be a winning trend.
However, this stuff is all subjective, and do what sounds good to you :twisted: