Better gear and more fillers will improve it. Although I still do occasionally run into moments when everything is on CD and all I can do is wait; those don't last more than a couple of seconds though. And generally I don't need to blow cooldowns during daily quests, unless shit hits the fan and I end up pulling a lot more than I can comfortably handle.
Happens mostly with those idiot shado-pan companions whose main goal seems to be to ensure your premature death by aggroing everything in sight.
I'm not into warriors stance dance and all that, and not really into dk with their rune regen. So decided to do a paladin. I like him. Although he feels very slow atm. But I'm glad that I can hear it won't be like that later
The end game goal is to fill every GCD with a skill, so there will be very few periods of watching your auto attacks, and you'll be stacking haste if you're PvEing so those periods will be even shorter
The ret rotation is pretty smooth in the end game. In Cata, I found there were awkward pauses but there is more holy power and few noticeable gaps in MoP.
While leveling, it takes a while to get some key skills. I would suggest you pick up protection as an OS and try some dungeons - it's not so different from ret and may be better for AOE. The queues are leveling dungeons are SO much shorter for tanks and it's a nice change of pace from solo questing.
ret rotation is as good as it's ever been at lvl 90, gets a lot better when you start to venture into the 20%-25% haste increase and higher. You can drop your cooldowns on Crusader Strike, Judgement, Exorcism and so on by a total of 5+ seconds with enough haste and that helps a ton compared to no haste at all. Once you start getting above 12-13k haste rating however mastery and strength becomes a lot better than just pure haste, keep your haste around 10-11k and you're good for almost everything. After you're at that point just go mastery (or str).
you will still get the odd span of time when you are doing nothing but auto attack . but only for a couple seconds at best , its way better than it used to be with haste being of actual value to use now