The 'classes versus free skills conflict' aside, every player needs to understand the skill system in order to create characters and start having fun. Of course, you can always fudge it and have a veteran player pick skills for the player, but that is a kludge, and certainly isn't a good 'new player experience' at all. If you were making a Facebook or other social game, and required players to find a veteran player to understand the game and learn it, you wouldn't get many players. That is a crude analogy, but it is appropriate. RPGs are social games.
What to do about the 'fun taxes' of pen-and-paper games? Well, for one, I am a big fan of simplifying rules down to their base components, and reducing complexity. We need 'green' roleplaying games, built with simplicity and new player friendliness in mind. I like my tower computers, but we live in a tablet world now - RPGs need to lighten up and become more useful and relevant. They need to be approachable without roleplaying being a requirement, in order to broaden their appeal. Most all of the European-style boxed games you can buy at game stores like Arkham Horror, Catan, and others do not require RP (but can be played as RP, or modded to do so). This leads to an interesting point:
You don't need rules to roleplay. Players do it all the time in MMOs without rules, all it takes is an active imagination. RP can be encouraged in the rules, but rules are not needed for the act. It is an interesting 'take' on writing an RP rules set - write the game first, and then worry about RP as an optional add-on component later.
A lot of games shift off complexity on the RP subsystem, as in, "Oh, we don't need rules for that, that will be handled through RP." Without the RP subsystem to shift rules to, all of a sudden, the problems in game design become clearer. How is a door forced or a lock picked? Some games leave it to the group to decide, but this is not ideal from a complexity control perspective, and also from a new player perspective. If European boardgame 'Explore the Dungeon' has a 4 in 6 chance to force a stuck door token, and pen-and-paper 'Dungeon RP Mysteries' leaves the entire 'stuck door' procedure up to the group - the new player is going to feel better with the former, and not the latter.
Wow, that rambled a bit. But I hope you have an appreciation of creating heavy rules subsystems in your games, and see these burdensome systems as a 'tax' on the fun of the game. You should never force a player to be a 'rules compiler' - someone who has to sit there and figure out how everything works together. The rules should present themselves naturally, and be clear and apparent from when they are read. Understand, all 'rules taxes' aren't bad - but they do take away time and reduce clarity, and you need rules to have a game. How many rules you need, and the point when these rules overpower the game - these are both things you need to think about as a game designer.