1)I use the similar skill rules from RMC2, where a certain number of ranks in 1 skill will apply to another skill (assuming that skill isn't higher to begin with). Is there an option to allow this with ERA?
There is a feature called "Rank Binding" which allows you to specify that a skill should take the ranks from another skill. This is only 1-1 for now, mostly since no one requested more of it.
2) How easy is it to add Classes and skills?
You should check some of the questions on the
advanced customization thread, the details are there. Short answer is, you can if you take the time to manually edit some configuration files. If you need additional details you can always add more questions on that thread.
3) is it possible to tweak progression bonuses for % in a skill per rank, or class bonuses to a skill per character level?
By default RMC bonuses are based on character level, and you can create your own professions manually and specify whichever bonus you want per level.
RMU uses a bonus that is +1 per rank, but that is not available yet in ERA.
As a general rule, bear in mind that RMC uses almost the same mechanics as RM2, so you should download the free demo version, start ERA for RMC, and see if anything is missing.