I'm by no means an expert so hopefully others will chime in, but here's what I think I know:
Spectrapure is generally good but pretty pricey. I buy their media, but didn't buy their units. BRS is well known as well as a good alternative (the no-name one I bought looks identical to their units).
I've never seen units with multiple membranes, though I suppose they exist. Usually they add additional pre-filters so as to get more gallons generally, but also cleaner water into the membrane so it lasts longer. The problem with that is membranes are not all that expensive, so whether the additional filter to place (and canister to buy) is worth it depends a lot on how bad your input water is. I've also heard that if you have chloramines (vs sodium hypochlorite) having more carbon blocks is better, and there are some chloramine-specific blocks as well, and some I think have membranes that are better with them. I didn't investigate that as I don't have chloramines.
Some units have multiple DI resin containers. That lets them last longer but I do not think it actually changes the recurring costs, as my impression is that DI resin converts so many gallons regardless (well, gallons at a specific input TDS).
You definitely want a unit that has a refillable (not just replaceable) DI media. I buy about 5L at a time from Spectrapure, and refill mine when I start seeing something other than zero TDS coming out.
You want to replace the prefilters when they no longer remove all the chlorine (and/or other stuff), OR when the pressure drop across it gets too large, OR (most people say) every 6 months. The latter seems a catch all as it's definitely a function of how much water you run through it, but I haven't found any good way to tell other than 6 months. I keep thinking of getting a chlorine test kit to see if what comes out of the prefilters is leaving chlorine in (chlorine kills RO membranes).
It is worth noting that RO water (without a DI stage) is awfully clean, usually in the 10-20 TDS or maybe better. There's probably no real need for the DI stage in freshwater at all. The RO membrane is going to remove 90-99% of most "stuff" in the water. I use one so I don't have to worry what the remaining 10 TDS is, but that's probably compulsive behavior rather than necessary.
I put a pressure guage at the input, and between the final pre-filter and membrane, so I could see if the filters were clogged. I've never gotten close to "clogged", the worst drop (when flushing) is about 5 psi for me and that's with 0.5u filters. So I'm not sure how important that is. It is important to know you have pretty high pressure; if your pressure is low (say 40psi, or maybe a bit more) or lower you might want a boost pump or your production rate will be quite low.
I elected NOT to go with the built in TDS meters. The handheld units are more accurate (they temperature adjust but most built in do not). What i did was put valves between the RO output and the DI input so I could get RO-only water out. That's useful not (just) for getting RO water, but after flushing or when starting up, I run the RO-only water for a bit until the TDS falls. When the pressure changes, RO membranes often back-up (in a sense) and get polluted water on the wrong side of the membrane, so the first quart or few that comes out is relatively high TDS. So each time I start up I close the DI output, open the RO-only output, and let a quart or so run off, checking the TDS with the meter. It starts about mid-30's, but quickly drops to low teens. When it reaches low teens I close that valve, and open the DI valve to let the water flow to the DI media. If you think about it -- 30 TDS water is going to consume your DI media three times as quick as 10 TDS (at least to a gross approximation).
I hear lots of differing opinions on flushing but I believe in it and do it each time when shutting down (briefly), starting up (longer), or once every 24 hours. I have no idea if that's a reasonable schedule, I just made it up to have some process.
I use non-color-indicating DI media because I have heard it lasts longer, and I don't worry if a few hours of exhausted DI media lets a few gallons of 10TDS water mix in. Not a big deal to me.
The media that came with mine lasted probably a third as long as the much more expensive DI media that came from Spectrapure - there is a difference (but there's quite a difference in price also; I'm not certain whether the cost per gallon works out, but I like changing it less so use Spectrapure).
Don't buy membranes too much in advance, they do not age well. Prefilters can be kept on hand. DI bulk media can be kept on hand also but it also has a life limit (I think they say 6 months or a year or so), so do not buy a LOT more than you need, but do keep some on hand (if you want DI at all).
The gallons per day is primarily determined by the membrane. The same physical unit can often double in volume with a new membrane, if you have adequate pressure. Unless of course it's already at maximum. Often you can tell by looking at the replacement parts.
Some flow restrictors are not very accurate. I got a 4:1 one for mine, and it was way off. I ended up using a valve and guessing (with occasionally measuring time to fill a cup with water from the waste and output). It's important to get at least the membrane's waste flow rate, e.g. if it needs 3:1 you need AT LEAST 3:1, having less won't properly remove the waste and limit its life and/or efficiency. Having too much waste water (up to a point) is just wasteful, not harmful. I like Spectrapure's concept where they can be adjusted by cutting a tube, but I didn't get any of those. At least I think ti was theirs.
Store the membrane soaked in water, which means when I shut down I leave the whole unit full of water, which makes it pretty heavy (I have a 5 stage). So if you plan to put it away somewhere be aware it's both heavy and might drip a bit.
That's about all I can think of off hand.
