I own one of each (MkI and MkII).  I'm practicing/gigging a bit more now than I have in recent years and wanted another amp to leave at another studio so I don't have to cart things around and load/unload (saves a lot of time being able to walk in with just my guitar and plug in).  So where did I go for a 3rd?  I got me another MkI.  I went round and round in my head, but in the end the MkI sounds better across the board than the MkII.  After receiving the MkI I plugged it in and was immediately convinced I made the correct choice.  I primarily use a Strat with one group, and a PRS McCarty (i.e. Les Paul type) with another group and it covers the gammit very well.  Re your Strat being a little to trebly:  I primarily go with 4 patches too, and with the same general setup as you.  BUT, I found the need to have a 'Strat' bank and a 'PRS' bank in order to accomodate the different tones of the guitars - i.e. I twaek the tones a bit for each axe).

I have several nagging little issues with the MkII.  Most annoying is the tuner doesn't work worth a crap.  Works great on both my MkI's (vs. same guitar, cord going into the MkII).  I've complained about this from day one of purchasing the MkII but have never gotten any response from Line 6 on the matter. I also don't believe my phaser effect is working correctly (more like a switch toggling on/off than a sweep of phase), and there are other inherent issues such as setting volume between channels and popping when you switch channels, etc.  Folks have been complainig for years now about these issues with not a peep from Line 6 about any resolution (i.e. don't expect any...).

The MkII shortboard sucks compared to the MkI.  Period.  On occasion I've used both pedals in the same weekend, back to back nights, and I much prefer the MkI - larger display, you can feel when you hit the button, and it's hard to accidentally hit a button by mistake.  The MkII shortboard you have to be very careful not to 'touch' a button or you will activate it (have accidentally engaged the looper going into a solo on a couple of occasions now - that was fun!).

I kind of feel like i was suckered into buying the MkII becasue of the added capabilities, which I really liked and wanted.  The MkII is definitely more capable than the MkI (meaning more tweakable), but if you add up all the little issues it may not be worth it.  A lot of folks are using the MkII and it suits their needs just fine.  I've been gigging with the MkII for 1 1/2+years now and am still trying to get some of the really nice tones I get from the MkI out of it (have pretty much accepted I won't be able to...).