Rule Number One: Rules are meant to be guidelines, not hard and fast. If a rule slows down gameplay then change it or remove it.
Rule Number Two: Scenarios should not be the be all and end all of the game. Don't stick slavishly to the scenario. If the players do something that will wreck the scenario then let them and spawn something else from that.
Rule Number Three: Let the players do things that they want to do as well as be guided by the GM. By all means warn them about doing something or use the "That's a brave thing to do" or the "Well, if you really want to do that" approach.
Rule Number Four: You are the all-powerful GM and can influence things in whatever way you want. If you don't like the way things are happening then bring in an NPC or event to change it. If the PCs are creaming the opposition then make things harder for them. If the PCs are getting slaughtered then make things easier for them.
Rule Number Five: At the end of a scenario, the players should feel that they have achieved something, no matter how small. Even if things have gone badly, point out that they are still alive or can be resurrected or whatever. If you finish one scenario on a downer then make the next one more upbeat and throw in some easy wins for the players. They'll appreciate it and so will you.
I don't have any problems with rules and gameplay, simply because I change the rules that slow things down. I use RQ3 as my starting point but heavily houserule it. I don't bother with Fatigue and Encumberence unless it is vital to the plot. I tend not to count Total Hit Points unless someone is taking the mickey and, in any case, I treat 0HP as unconscious and going past your normal HPs negative as dead, so someone with 15HPs only dies if they go to -15 or below.
My players control their own HPs, Magic Points, spells and so on. I've enough to do without keepig track of everything. Similarly for Experience Points - they roll them in front of me and sometimes ask me to witness POW and rolls that are important to them, but most of the time I trust them not to cheat.
If someone cheats now and again, I don't mind as that's what they enjoy. If they cheat all the while or their cheating annoys other players then I punish them.
I roll all dice in the open and insist on players doing so as well. I never fudge dice rolls, but I sometimes "forget" to do things, such as rolling for poison until the Hydra is dead. Sometimes the players let me forget, other times they gleefully point out that someone else's PC has taken poison damage and "shouldn't he be rolling?".
When I have a choice between something that will bog the game down and somethig that will speed the game up, then generally I choose the latter, unless the former is vital to the game.
Above all, the games are about having fun and enjoying ourselves. I like to think that we get together every week to socialise and also to have fun in the games. Occasionally it hasn't happened and a player has left, but that has been because they wanted a different gaming style and a different gaming system.
