There are a few things I have players do that provide a uniqueness and more fleshed out history.
I let players swap out Base Spell Lists (obviously with approval, but our group is reasonable enough I don't have to worry about it much), most commonly with Magicians, Rangers, Paladins, and Clerics (a la Priests from the Channeling Companion). Rangers I'll even let change realm. I've got a profession or, alternately, a set of Training Packages that are intended to modify Magicians (and sometimes other professions) that orient them more towards elemental magic. I have a more general Elementalist profession that concentrates on most of them, but also an Elementalist Training Package that lets you add two spell lists of a specific element to the character. For the TP version check out RMQ's 1 & 2. I never published the full on Profession version. Didn't want to step on the toes of the Elemental Companion in that respect.
I converted Everyman and Occupational skills to a per rank bonus (and then often mess with what those skills are). So you get your flat, upfront, RMSS profession bonus plus a +1 per rank bonus for Everyman and +2 per rank bonus for Occupational (I would probably never allow these to relate to a direct OB skill however).
I'll have the character create a backstory vocation and provide free skill ranks in roleplaying skills (I'd assign them, they don't just get DP to spend or anything). So, for example, a character might have been a fishermans son who grew up to be a sailor before moving on to 'adventuring'. I'd provide that character with non-combat skills related to those things which would then come in handy during sea based adventures. This encourages more roleplaying in my opinion. (If I ever write my own system it will split combat and non-combat development into two separately developed groups with their own pool of DP).
Most directly related to your OP is that we've converted plenty of RM2 professions and spell lists over to RMSS. Using an existing RMSS template I just see if there are any specific skill costs I need to adjust up or down. Profession bonuses are easy to convert and everyman/occupations skills I'd just assign as appropriate (especially since I often mess with the normal RMSS ones anyhow). Spell lists often require some shuffling around of spells to bring the power level more into balance with RMSS and I usually try to fill in the blank spaces too.
But, in the end, Talents/Flaws often can do the same job. You just need to (imo) eye-ball the costs to make sure they are balanced. Some of them are not well priced at all (again, imo).
