Kudos to the OP for the well thought out post! I'll try to play devil's advocate on some of the topics you've brought up, bearing in mind that I have played neither Eve nor WoT and really know nothing about either game, but, I have scoured and read most every thread about what the devs' vision of what they want MWO to be.
Lesson #1 - I agree with you on this point with Cbill, loyalty points, map visibility, small (say 1-5%) discounts on repairs, but your use of the term "special" mods and mechs is a little worrisome. I can easily see this turning into a flame war about tactical advantage if done wrong. Last I heard they were working on achievements being available post launch sometime, that could be a good solution for some of it as well. On a side note, money for the cash shop should be very rarely given out during game play, if it's given out for everyday gameplay it WILL BE manipulated in some way, shape, or form.
Lesson #2 - Good idea as well but limitations will have to be put into place on how much each merc can hold and how often they can try. In my experience, if given the option, the larger guilds will take everything they can no matter how "poor" the incentive. Often relying on their superior numbers to hold it all and just outlast any attempts to take it over or use their numbers to retake it if lost. Coordinating actual combat times for planetary capture between mercs could also prove inefficient. Merc X owns a planet so they keep stalling in the hopes that merc y just gives up and tries for another planet is just one example.
Lesson #3 - Although the concept of this sounds good, I'm just not sure a single massive merc group is going to be a powerhouse in the ways you think it's going to be for MWO. MWO will not have a perpetual universe that any one unit can dominate and control, canon won't allow it. Maybe down the road if they speed up the timeline it will be a valid option but with status quo it won't. I agree in the sense that you want to be able to fight alongside with your friends and that's how it should be, but at a certain point I think it will get to the point, "Hey we have the biggest merc group in MWO, even bigger than some of the houses!" But at what cost? If everyone is your friend, then who will be your enemy? I, for one would rather be in that merc group of 24 players that can 9 times out of 10 beat that merc group that has 500 members.
Lesson #4 - This discussion has been raised many times over in one form or another on the forums. How close is MWO going to stick to canon is what it eventually boils down to. This won't be a truly sandbox kind of game, otherwise they will have to do a reset eventually when one house, clan or merc takes over the entire IS. They're going to release MWO as a minimum viable product to begin with, but I believe post launch they are wanting to eventually incorporate more of a meta game strategy to warfare as well. I would love to see interplanetary supply lines and be able to capture and hold enemy planets with pre-determined force parameters for offense and defense, but that is a ways off for now.
Lesson #5 - I believe a lot of people here eventually want something like that in some form, again, how close to canon they remain will be the base for any restrictions placed. That's one of the best things about BTU fluff is that there is room for wiggling around in, but what you're proposing is very very rare for merc groups to accomplish in any degree. Side note, one of the easiest ways to lose players is to have them pour everything they earn into their "world" and then lose months, if not years of work overnight just because someone else felt like taking it on a whim.
Lesson #6 - I remember reading that contracts will be controlled by the devs (most likely some sort of program) at launch and further down the road possibly by higher level house members. Other than that the devs haven't given us much in the way of details about bidding and contracts.
TLDR: You bring up many good and interesting points and certainly a lot for the devs to think about. I would love for a lot, though not all, of your ideas to be implemented! I've tried to play devil's advocate here and not sure my thoughts came out exactly right given the time of this writing and the need for sleep
It sounds like you want MWO to be a sandbox mechgame where the biggest (and best?) can rule the universe. That would make for a great game and I would be all for trying it but I don't think MWO will be that game and still be able to stick to its roots and canon in the BT universe timeline.