You could combine both approaches. You pay the maintenance costs based on the unit value (Jayof9s/Ralgith), while also applying the maintenance rolls. You keep them at once a week, but allow for a "generous" (YMMV) modifier, so that you don't have to replace cockpits every week. The shifting quality modifiers would be disabled for the reason mentioned by Jayof9s.
IC explanation would be that mechs (and other vehicles) need maintenance on two levels: "routine" and "extensive". A fried circuit or a nicked myomer don't necessarily need the entire unit (cockpit, leg, ...) replaced. Those are covered by the maintenance costs. But every once in a while, a part may break down and require a replacement, which is covered by the maintenance rolls. This part is more rare, unless your warriors are total dolts and scrape the sides of the bay everytime they power up their ride. :P Of course, being in the field or safely tucked in a dropship does make a difference, but that's something that MEKHQ already takes care of.
This might be too expensive (perhaps leave the percentage based maintenance payment off?) for a new mercenary unit, but it does dull the edge with regards to the modifiers. The exact maintenance roll modifier is a personal thing in any case.
Just two C-BILLs from a (very) green player. :)
