I wasn't a fan of the Ultimate's seating system that everyone else seems to rave about, but mostly since it didn't give me the back support I wanted for pedaling. I LOVE the dual height seating feature of the Commander. The "Captain's Perch" allows me to vary my position and paddling style on long outings and makes getting in and out as well as standing in the boat easier than any other boat I've tried, and I find the comfort of the main seat more than adequate. You sit farther forward in the Commander so it seems like you are in a smaller boat than the Ultimate, but the rear storage area is positively huge. My broken down paddle would not fit in that area of the Ultimate but lays flat with room to spare in the Commander.
One thing I dislike about the Commander is the floor. It is very irregular due to the keel running down the middle of the boat. I made floors for the front and back out of treated plywood and outdoor carpeting so my stuff (including my dogs) have a flat stable platform above any water that gets in the boat. The Commander has more freeboard than the Ultimate which is comforting but would typically make it harder to control in the wind, however due to the center keel molded into the boat it tracks straight and true even in high wind.
I tried on two occasions to re-enter my Ultimate 14.5 in deep water and was unsuccessful. I was able to re-enter the Commander relatively easy from deep water, which is an important safety feature. I think the difference may be related to the increased freeboard of the Commander. On another safety related note I found in both boats that the tunnel hull design makes bailing with a round quart sized or larger open top vessel much easier and faster than using a standard kayak bailing pump.
I like the fact that the Commander is pre-configured for a trolling motor as I plan on taking advantage of that in the future. It's also pre-plummed for the necessary steering cables and would be a relative breeze to do it yourself, unlike most other kayaks where adding a trolling motor to the back requires significant custom fabrication of mounts and cables, etc.
I really like the Commander 140 but I would probably have been happy with a standard Ultimate 14.5 as well. I had just gotten tired of all the useable space I lost with the pedal drive model. They are both high quality and quite similar but the Commander does have a few touches that I appreciate over the Ultimate. Your mileage may vary.
I have no trouble maintaining 4-4.5mph in the 145 for long stretches, although the power required to go any faster is logarithmic in scale. I can reach 6mpg but only at the risk of cardiac arrest! I use a Greenland style paddle.
I absolutely love the boat. I've only been paddling for two years but I've tried several other types of boats (17' fiberglass boats, and one skin - on frame) and none are anywhere near as comfortable and versatile. I love the amount of gear I can put in it. An 8 day trip down the Suwanee river was no problem. I don't have to worry about scraping it on rocks or oyster beds.
Mine has the rudder which I recommend. Once I got used to it my feet almost subconsciously steer the boat while I concentrate on padding most efficiently. Very effective also in windy conditions as well as side currents in winding rivers.
You cannot beat the seat in this kayak. No other boat (except the Tusnami 140) I've tried approaches the same level of comfort and this makes being in the boat for hours a non-issue. The boat is also very stable. I have not even attempted to learn to roll in this boat. It is so stable I don't think it would roll well and unless I put myself in a very stupid situation, I don't think it would ever be necessary.
I have not had any rear hatch problems with my 145, although we had 2 140s and had trouble with the rear hatches on both. One thing I do not like is that the seat does not move close enough to the rear of the cockpit opening making attaching the spray skirt quite difficult. I find it almost impossible when attempted solo in rough conditions.
Another thing I would change is that the cockpit is too wide for me. I need the extra length in the 145 but I have trouble becoming "one with the boat" due to the wide cockpit. This is exaggerated by the fact that one has to have space for the legs to move to work the rudder rather than have the knees firmly wedged against the sides of the cockpit. I still think the rudder is worth it for the environments I typically paddle. This is not a problem with the boat itself, just things that are challenges for me.
If you like to paddle for extended lengths of time and/or kayak camp the Wilderness Systems Tsunami is hard to beat. I recommend the 140 for normal size paddlers and the 145 for large or tall paddlers.