For heal skill, I use the signet. It isn't perfect, but the other two really need some work for exactly the reasons you described. Healing is decent, recharge is pretty good at at 24s if you run the signet recharge trait @ 10 radiance (which I usually do), and I really like the passive condition removal. Once every 10 seconds doesn't sound like much, but it actually translates to a new condition being removed from you after 5 seconds, on average. Prayer to Dwayna looks interesting, but as you pointed out, not available to my Charrdian. But hey, at least I LOOK tough!
As with anything build-wise...below stuff fits my play style. Any additional ideas are welcome!
Tl;DR: On staying alive...Guardian doesn't really have any single uber heals outside of Tome of Courage, but they have so, so many ways to mitigate damage while buffing allies...so at least with my play style, it's "I still have skills in reserve? cool, GET OVER HERE!" or "active heals/prot running low...should probably start kiting, staffing, while these beasties recharge". Tons of boons and damage reduction let you roll like a SY build in GW1 - you are able to use small heals because that's all you need. I also like shouts because they are instant, such as the oh-so-useful "Stand Your Ground" that will instantly get you up from an otherwise-fatal knockdown.
Ultimately, you should never, ever die as a guardian while you still have unused skills. It's less of a function of your health bar, and more of a function of getting away when you're running low on things. I hope that sums it up...I am not a terse man.
General Melee
This is just random stuff I've learned so far that would pretty much apply to any up-close fighting, even if someone isn't a melee spec. Probably the most useful thing I've learned is to pay attention to who is being attacked. I probably mitigate more damage here than any other way. This stuff might be obvious, but it has surely helped me! Would love to hear anything I missed.
Don't stand beside your ally! - If you attack two enemies standing beside one another, you hit them both. The same is true for enemies. We all love each other and all, but standing on top of your buddy means that the enemy will hit you both when attacking either, generally meaning double damage. Even worse if there are more of you. Instead you should...
Move behind/beside/whatever an enemy - This avoids all damage from most attacks, and has the bonus feature of making it very easy to see who the baddie is targeting. A lot of the time you can simply stand there and unleash just because it's the other poor sap who is being targeted. Should the mob turn around towards you...it's time to..
Move evasively - Many attacks in this game are slow and you can avoid them as simply as circling the enemy or doing a figure 8. Enemies also will often chase for a teeny bit, reducing the amount of attacks...good old kiting. Enemies do not move evasively, on the other hand, so you can continue to pound on them. Some people (not me) like binding their Q and E key to the A and D keys as well to make this easier. "Figure 8" (not sure if that is a good term) is good because you can run through the enemy, ducking behind them as they attack. Your toon will instantly turn around to attack without missing a beat.
Holding the keys to evasively maneuver while simultaneously using skills can be difficult...though it's sometimes more important to move and auto-attack than it is to fire off an attack skill. One thing you could do is click the skills while moving. I cheat with my Razer Naga - all 10 skill buttons plus dodge right there on the side. Great mouse!
Dodging - Yeah, obviously dodging well is important...that takes practice along with knowing the area you're in. Obviously you want to use this for the bigger ground pounds/etc, but it's very useful for "getting out of Dodge". (reverse "yo dawg"?)
One fun trick with dodging is to jump at the same time. Not only does this make you look and feel like a superstar, but you actually gain total speed in doing so, because the air time + dodge speed moves you further than a regular dodge would. Flip jumping while running around will impress your friends and is great for those frequent trips from the Trade Post to the Bank. Bonus points if doing off a ledge (more airtime) or over an obstacle. It takes a little practice to get the timing right at first, but once you do it's pretty easy to do consistently.
Speaking practically...are you in mortal danger? Why not double back-flip out of danger while simultaneously whipping out one's staff to lay down some wards? Also, you can flip through cripple! Same goes for any leap/movement skill. Between air time of flipping and average 5s passive condition removal, it is rare that cripple actually slow me down at all.
In short, melee in GW2 isn't about being punched in the face so that your friends don't have to...they'll just punch you down and THEN hit your friends. Instead, stay healthy and be a hero if they go down. Two are better than one, because when one falls down, he can pick the other back up. Guardians are good at this.
Speaking of...
Guardian Stuff
Here's the stuff I'm running, not always all at the same time. As I've mentioned, I like shouts, and I like virtues. All of these things can be cast instantly. Nice. I typically run this bar:
Signet of Resolve, "Save Yourselves!", "Hold the Line!", "Stand Your Ground!", and Renewed Focus.
Current traits are 15 radiance (reduced signet charge), 30 Honor (reduced shout recharge, protective reviver, Pure of Voice to convert a condition to a boon for me and allies). Planning on probably going 5 honor rest Virtues.
Reviving - There are two very nice traits in the Honor line for this. Resolute Healer casts SoA as soon as you start reviving a dead or downed player, pushing foes away and stopping projectiles. Makes it VERY easy to res. Protective reviver gives both you and the downed player 10s of aegis, protection, and regen once they're up. Nice. Using both of these makes you an absolute resurrecting machine. If your teammates die often enough, you don't need any other skills for protection!

If not, you're probably doing well as a team anyway. I've heard healing power helps with reviving, have not yet confirmed.
Aegis/Virtue of Courage - Lots of sources of Aegis. Aegis essentially gives you one free block. VoC should have given you a free one before battle; get in the habit of using it again when you need it. Don't be like me for the first 50 levels and let your virtues be completely passive. With Renewed Focus you're taking three aegis into battle, even before anything recharges. This is super helpful against the hard-hitters. With 5 points in virtues, you also get protection when using VoC.
Signet of Resolve - Not a lot to talk about here...I hit this about when I get half health. At that point I've probably already spent SY and HtL, so it's time to cartwheel out of there. In fact, you should probably already be bravely running away.
"Save Yourselves!" - Seriously, every boon but stability for 10 seconds + Virtues bonus? Sheesh. In low-danger environments I use this to boost damage. In high danger I will use this (after spending Hold the Line, due to recharges) as a prot/regen. I'll use these skills after I start to lose a little health...don't want to dip too low and get desperate. Zipping around an enemy is never easier than when you have 10-13 seconds of swiftness.
"Hold the Line!" - Affects allies, prot and regen, decently large range. This is the first thing I use once I start to take damage, due to helping allies and a lower recharge than SY.
"Stand Your Ground!" - Knockdown and the like are super, super dangerous; you can die before you get up. Not anymore. You don't even need to pre-prot this puppy, because it's a shout. I've tested and confirmed that this will instantly get you back on your feet, should you get knocked down. Retaliation is nice when a big enemy ground pounds.
Renewed Focus - I can't speak for Tome of Courage; will be unlocking soon. Tome of Wrath is fun with the KD, but losing out on heals and res is awful...found myself seldom using. I like RF. If all other options fail, hand jam your F1-F3 keys at the same time and then cast it...recharges them and makes you invulnerable for a few precious seconds.
All in all, I try to use protection when I need it, don't use anything if I don't (standing behind target), etc. By moving around and evading, it's rare that the bag of tricks is coming up empty.