Hi Craig. It's Tom (from Chelsea). I'm replying to your email and decided to post here. It's nice to see that your pond looks so great. Quite a beautiful urban oasis you've created. kudos!
Mine is also doing very well. By your description, it seems you followed an Aquascape type of water circulation system (and algae control) for the swimming area, and adapted David Pagan Butler's air based water circulation system for the planted areas. As you may recall, I went entirely with David's air concept. Both approaches work, but I believe David's is equally effective yet simpler, less costly to install, and less expensive in terms of electricity cost. I don't regret it at all.
You say your water is clear, so your overall ecosystem seems to be working effectively. It appears that your new goal is to have a clean bottom that is easily vacuumed, and a blue color liner more akin to a conventional pool in most part to make the swimming experience more desirable for your kids.
First, I agree that installing pea gravel was a mistake which you have now corrected. I didn't put anything over my EDPM. As for what to do next?.....I say, nothing. So, I agree with the advice you've been given by others here. Don't even try and install anything over the existing liner whether it be a blue glued liner, netting, concrete, whatever. If you do, you will be sorry and end up with more problems and maintenance than you bargained for. The reddish coloration is likely staining from the pea gravel. Whether or not it goes away, it will at least diminish when the natural biofilm returns.
Your liner and mine look similar, including the creases though my shallow end is very smooth, and mine doesn't have any reddish staining. Even with the creases, vacuuming shouldn't be a problem so long as you accept that this is a pond and not a conventional swimming pool where you see EVERYTHING! My water is perfectly clear to 8' deep, yet because of the black liner, they barely show if at all. Visitors don't even notice. This is a big reason why you do not want to have a blue liner. As has been said, in a natural water environment, it won't stay looking blue for long anyhow, and because of that, could even look horrible, at least while it transitions to its eventual state. Personally, me and everyone I know loves the natural lake-like clear greenish hue that a black liner creates.
I have two vacuuming approaches.....a homemade one that I constructed, and an Oase Pond Vacuum that I bought. I use the Oase for most of the pond area including the planting zones, but as my deep end in about 8' deep, the Oase won't draw from that deep, so as must use it in the shallow areas. This is where my homemade system comes in and with it, I'm able to recirculate the cleaned, warm pond water back into the pond.
I think you mentioned weekly vacuuming, and I have to ask why? I do a good vacuuming upon opening and closing, but remember that unlike a chemically induced pristine clear blue pool, a pond, even a swimming pond, is a natural (more like engineers simulation) environment where cleaned perfection should not, and cannot be the goal. A slippery (bio)film will sit on the bottom more often than not. As people walk on the shallow bottom, the biofilm will kick up and make it seem that there's gunk in suspension in the water, but it's no different than what one would see with eyes open when swimming in a lake flailing around. Occasional light vacuuming especially in the shallow areas where swimmers walk/wade should make it ok, but some people may find it slippery or 'icky' regardless because they're not used to such a swimming experience, especially kids, but it's something that folks just have to accept. It's well accepted at my pond. If you don't just accept it, you'll drive yourself nuts. If the plants are healthy, algae is under control and the water is very clear (periodically tested), that's as much as you can ask for.
The only thing about mine I would've done differently is to have left the regeneration (planting) zones deeper, like 2-2.5' rather than the 18" that I did, especially closest to the edge of the swimming area. Note that I filled my planting areas with layers of sand and pretty river rock. If I would haveleft deeper, I would've been able to leave all the lily tubs where they are rather than having to move them to the bottom of the shallow end for the winter. No big deal though, and worth it. Using tubs for all my plants, I can control the plant population so it looks like I'll want it and not be so wild and unkept looking. Personal preference though. Last season because it was so dry and hot for so long, I did have a string algae bloom. I'm working at solving this by getting a lot more plants in the planting areas by separating out my existing lilies into many more tubs. This should give much better surface coverage to minimize algae.
So, I advise to just leave well enough alone, fill it up with water and enjoy. Don't even try for it to be a conventional pool. The kids should just have to get over it.
Good luck!
Tom