I do sort of see what you mean. The 12ft is great and they do have 2 nice big shelters, but at a certain point these wooden structures do start to look a bit sad! The area itself looks great and I'd probably want to keep it where it is - like you say it's protected from the sun; but it definitely comes with the downside that it never looks sunny and lovely and lush. The cold floor could be helped by laying down rubber stable matting providing your bunnies aren't big chewers, and as others have suggested I think covering the tops of the runs with something waterproof would be good. Even clear tarpaulin would be great - I'd stay away from the blue stuff as it's not fully waterproof compared to the clear stuff.
Personally if you're already looking into buying a new setup anyway I'd be tempted to say that might be easier overall than sprucing up this setup. Like the others I think an aviary setup would be great. You can buy the panels from here, among other places:
http://www.happyhutch.co.uk/aviaries-aviary-panels/19g-aviary-panels-detail, plus a door:
http://www.happyhutch.co.uk/aviaries-aviary-panels/19g-aviary-panel-with-door-detail. Local builders will often do them too for you, and may even erect them for you. I'd definitely want to add some plywood (painted with cuprinol) or corrugated roofing sheets/polycarbonate twin walled sheet to the top to provide protection from the rain from above - I find it makes a big difference as the underneath stays a lot more dry and they can use it more weathers. You could then put in those 2 lovely big hutches you have, if you cut the top one off its run, and you'd have 2 massive cosy shelters for them.
Another option would be to get a nice big run and attach each hutch, at floor level, at either end. The bunnies would enjoy that as they feel safer having 2 exits or bolt holes, so that would be a fantastic setup too. Boyles pet housing do some lovely sizes runs and I'm sure he'd do specific sizes to suit you:
http://www.boylespethousing.co.uk/rabbit-housing/rabbit-runs.html. He also does amazing looking aviaries with clear pricing, and the option to have a timber and felt roof too. Again I'm sure he'd do custom sizes to suit your space.
Like you've said, I think it'd be a great idea to keep everything on one level for your partially sighted bunny.
If money is an issue when it comes to size for the aviary, as I know the costs can really rack up, a good option to maximise the space would be to attach the hutch to the aviary and not have it actually inside where it takes up the space. I'm a big big fan of the runaround products - they're very secure, and bunnies enjoy them. These two would work well:
http://www.runaround.co.uk/products/connection-kit-4,
http://www.runaround.co.uk/products/bridge-link. Alternatively just because of your bunnies eyesight, one of these might work better if you put it as flat on the ground as possible - just because the wooden construction won't shake like the pipe does when bunnies scuttle down it:
http://www.boylespethousing.co.uk/accessories/joining-tunnel.html,
http://www.boylespethousing.co.uk/accessories/large-timber-tunnel-hinged-roof.html.
If the floor is still quite good condition in the high hutch it'd be worth laying lino down on the floor and sealing around the edges with silicone bathroom sealant to prevent leaks etc. This will give them a cosy floor which never gets cold, which will be nice for them. Alternatively the rubber stable matting would also work in there!
I'm not sure where you give your hay to them at the moment, but bunnies love eating while they poop so they take really well to litter trays and can spend a lot of time in them. Underbed storage boxes (without the lid) work well as a lovely deep litter tray - put some litter/substrate/newspaper in the bottom and put loads of hay in. They'll love digging around for the best bits of hay and it really takes up a lot of their time and simulates natural behaviours. In a nice big setup like that I'd be tempted to have 3, or certainly 2
The hooded litter trays for cats work well for outdoors as the hay doesn't blow everywhere, I have this jumbo one for my two:
http://www.amazon.co.uk/Catit-Jumbo-Hooded-Litter-Tray/dp/B0057XF6U4. With one of your bunnies having trouble with his eyes it may be a good idea to try potting trays - a lot of other people use them for partially blind or disabled bunnies. With no lip, your bunny will find it nice and easy to get into:
http://www.amazon.co.uk/s/ref=sr_gn...&keywords=potting+tray&ie=UTF8&qid=1405860583. The bigger the better with litter trays, imo!
In terms of extra stuff to add, bunnies enjoy tunnels and both of yours should be able to enjoy them easily. They sell them everywhere really - the top 3 on here are firm favourites with most bunnies!:
http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias=aps&field-keywords=rabbit tunnel. I persnally love the 3 way one but don't get to use mine that much as my run is only 8 x 4, and it's a little squished. But in a big run like yours it should fit really nicely. The plastic one is great too, although bunnies can chew it so definitely keep an eye when you first put it in.
Bunnies tend to love toys as well. Wicker etc is great to chew, as is wood, and there are loads about. Wilkinsons or viovet sell all these cheaply. I tend to only put these inside a hutch though as they get a bit ruined outside with the rain! For outside, plastic toys work great. Babies toys are often quite good... things like this
http://www.amazon.co.uk/East-Coast-...e=UTF8&qid=1405861504&sr=8-4&keywords=teether or this
http://www.amazon.co.uk/East-Coast-..._sim_by_3?ie=UTF8&refRID=15WZJBPA3B9Y4JJAYQH0. Anything that they can pick up and throw around. Avoid anything with those liquid bits meant for freezing, or anything with rubber on. To be honest the best place to find the cheapy versions without extra added rubber etc is the pound shop :lol: You can get these type of things for £1, and you can make 3 good size toys if you link bits together:
http://www.ebay.co.uk/itm/Baby-Lear...?pt=UK_Toys_Games_Toys_CA&hash=item58ad25c83b. Things that make noises might be good for your partially sighted bunny too:
http://www.wilko.com/small-animal-toys/wilko-jingle-dumbell-for-small-animals/invt/0303655.
Another option would be to get some grass seeds and grow some big pans of grass. You could then put these in every so often for them to nibble away at - it's fun and really good for them. Bunnies love digging too, so a digging pit might be a great idea, but that's something they'll probably end up doing in their litter tray if it's big enough so you could combine that. If you do want to introduce a litter tray many people use kids wooden or plastic sand pits, and either use kids play sand or soil. I personally prefer soil just because we definitely know it's safe, and I worry about bunnies getting sand in their eye.
Basically with a few additions such as litter trays, toys and tunnels; plus a bit of painting and a roof your setup is really great! It offers great space, and is protected from the sun. But if you do want to replace it I'd definitely go for an aviary or a big run, and still use the two hutches (unless you really want to replace them).
P.S sorry for the essay :shock: Hopefully it's of some help