Nightblade, what I found was the training packages he was using with the RMC character. His stats all jumped-up out of proportion with the other stats of the group and he had far more DP to spend per level than the others had. He had bundles of skills that he wouldn't have been able to purchase using the RM2 DP costs and purchase method.
I ran into the same issue when I ran my weekend campaign last fall. I kept telling the two first-timers that I would help them roll up the PCs. If... IF... they really wanted to buy any books, make sure they are RM2ed. NOT RMC, RMFRP, RMSS. Make sure RM2. In fact I told them specifically to get RMC-II and Elemental Companion and forget anything else. I sent text after text, e-mails reiterating this. They insisted on trying it on their own and ended up doing so with the wrong books. It got to the point where they texted me and asked which packages I was allowing. I had no idea what they were talking about. I asked which book and he said Hard Knocks.
I use the RAW as closely as possible for simplicity. I do use the very simplified Initiative which is simply roll, and go down the line. I don't do all the phases. Combat bogs down as it is and having 7 phases to manage each time is too much. A higher initiative can hold his action until later in the series if he'd like.
I do allow every skill in every companion. If they want to spread out their DP, they certainly can. No one has ever taken Hygiene, Weapon Bugei, Stilt Walking, or Animal Husbandry, but it's there if they want it.
I am in the exact same boat you are in too. My very first exposure to gaming was RM2 with the greatest group of guys I ever gamed with. We had fall on the floor laughing sessions and it was all RM2. Since then, I've tried different systems and each has it merit, but RM2 is simply my favorite even after 30 years. I love World of Darkness, I had a blast with GURPS Supers and Toons, I've played D&D and Pathfinder, but RM2 is my go-to for GM-ing as I know that system best. I've run Vampire:tM as it's my next favorite game, but I'm no where near as fluent or comfortable running those sessions, and I've read those books cover to cover just for fun several times over. I picked up V:tM when it was first released too.