Im not 100% happy with how health or whatever is displayed in the above shot, its messy. though I think most RTS etc have something similar, Any ideas for a better method?

Yeah, the health meter shapes look a bit messy, probably because they float freely over the bottom circle and are wider, so they don't seem fully connected within the unit. There are many ways to connect them visually though, I really dunno what's best but here are some ideas:

The circle itself can be a meter (either circular or horizontal).
- Avoid the z-axis though as it can become obscured by the unit itself.
Or a slight arc shaped health would fit better above the circle.
Or a square around the unit makes the meter line in with it naturally.

By the way, how much of the game has green grass? The green meters almost blend in with the grass, have you considered another meter color to emphasize it?

Cool creatures by the way.

I agree with turning the circle into a HP meter. It can work like a pie chart. That way it doubles for a target indicator and an HP display. I would also agree that changing the color to not blend in with the background so much would be good. Red is typically seen as the "health" color, so you could run with that... or even have things color coded for grouping or whatever if you really wanted.

edit: Also, for visibility purposes, sometimes it might be hard to see the HP of a character if they are big and covering most of the circle... a way around this would be to bring the HP circle to the front (over the character) when the HP changes, and then drop it back after a couple of seconds.

I did the circle as HP indicator for a game I'm working on, although mine is entirely 2D tiled rather than isometric. I chose two distinct, concentric circles: one for selection and one for HP. The HP circle fades in and changes to red as it goes down, so normally the HP circle is not even visible. You could also experiment with different line styles, such as dotted or dashed. Your current approach with the bar on top could work, but you might try reducing the width of the bars and changing the color/style to differentiate it from the selection circle.

If you look above at the center guy you will see I did also try the circle as the HP guide, I didnt like that either.
I might try another idea I thought of last night, draw a halo around the creature

btw the graphics arent mine, just placeholders

Here's a possible way to make the circle as lifebar work: have the colour correspond to the team it belongs to. If you made it a bit thicker (possibly semitransparent to avoid obscuring too much) you could leave just an outline where it's empty, removing the need for black and ensuring the team colour's visible even when health is almost depleted. That way, the circle can double for selection purposes and you have less clutter; it also gives a natural way to see the health of enemy units without the confusion of their lifebars being the same colour as your units'.

If you try the circle as the meter you have to keep in mind what is visible. Have a selection circle as normal, then have a thick arc lining the outside front of the circle. Not even the front 180°, more like the front 90° - 120° as a life bar curving with e selection circle.

Another approach is to use the whole circle (making sure the circle is big enough that you can always see it under the unit). Fade in red (filling the circle) and then slowly start it pulsing when it is fully faded in until it dies. This would be less exact looking for the player so its slightly more obfuscated as to current health status.

Well like I said Ive tried the circles and didnt like it
heres what I came up with (quick hack) color darkens (or fades) depending on health

Also worth keeping in mind that very few games actually display health bars all the time - for instance, StarCraft only displayed health bars above units while a specific key was depressed, while selecting a unit would display its health constantly in the HUD.

I think that new way looks bad, but that's just me. I think making it into circles like how you have the little circles in the original picture would be better. Take out the bar, then make the circle turn from green to red to indicate life.