I would just like to note that JDale and the developers of RMU do address some of these issues, and offer a range of options for dealing with them that I think are the best Rolemaster has been able to offer. Jdale has mentioned these above, but I think his post has gotten a bit lost in the animated (and engaging!) discussion.
To address the issue of the Fighter who picks up an unfamiliar weapon: Characters in RMU now get proficiency in categories, so if it is a weapon of the same category (e.g. a Claymore instead of a Great Falchion), then the Fighter already has full proficiency, because both are in the Greater Blades category and very close in the way they are used. If the weapon is from a different category, the Fighter still has other options. Fighter can use the (now core) similar skills rule, meaning he can wield the new weapon with as little as a -25 penalty, if the weapons are judged to have a similar skillset. And if all else fails, the Fighter can also take a level to familiarize himself with the new weapon by buying multiple ranks at level up (and for a Fighter, this will be relatively cheap), which is also now a core rule.
To address the issue of the Fighter vs. the Thief at a Subterfuge skill: By tying the professional bonus to the actual number of ranks developed, RMU allows the Thief to be better at a skill like this, which is associated specifically with his class, but how much better will vary considerably depending on how much the Thief has trained in the skill. At low levels and low skill ranks, the difference will be less than at high levels and skill ranks. Personally, I like this better than previous flat level bonus or up-front bonus systems, where there was no inherent link at all between professional bonus and the actual number of ranks developed.