I'm a used car/truck/Harley and new trailer dealer in MO. I also have vast experience moving HD's all across the nation. Here is what I have learned;
1) Double axle is THE way to go if you're hauling further than just around locally. Not only will the trailer pull better (not as much sway) but tandems typically are set up better. They will usually have a 2 5/16" ball instead of just a 2". Tandems generally have brakes (on both axles) and an emergency brake option so if the trailer comes unhitched the brakes automatically deploy and keep the trailer from passing you (not a good thing). Single axles are a bitch if you have a flat and most single axles don't have brakes. Many times single wheel trailers can even flip when they're pulled by a smaller vehicle and a trailer tire blows out. Again, the key here is if you're just gonna pull around town or if you're gonna use it like I believe you will. Also, you'll not find many 7' wide trailers with only single axles.
2) Low-Profile is THE way to go if you're using the trailer pretty much exclusively for bikes. As has already been stated they do help with fuel mileage - even when compared to a higher-profile with a V nose. Low profiles with the V nose are especially nice as the V also makes a great place to hang some cabinets, clothes rods, etc. However, if you plan on using your trailer for bikes AND for cargo (ie, band use, moving, etc) I would suggest that you go to a taller trailer with the V-nose. If you are using a low pro for cargo about the first 3 or 4 times you crack your head on the door opening you'll be wondering why you bought one so damn short. However, if mostly you are driving bikes in and out, you will be very happy with a low profile model.
3) Buy yourself two nice drive in, auto lock wheel chocks. I sell the Condor brand (
http://www.condor-lift.com/) as I ran across them several years ago at Daytona Bike Week and I wouldn't be without one now. The main advantages are that one person can drive it in the chock, get off the bike (without putting the kickstand down) and tie it down. Also, instead of putting so much pressure on the forks and fork seals you can tie the bike to the rear pegs/footboards and just pull it forward to keep the bike from pulling out of the chock. The Condors also are removable for when you want to haul something other than bikes and they are adjustable to fit several different front tire sizes.
4) Side Door: A MUST! When desiring to check your load, it's a lot easier to go thru the side door instead of letting the whole back gate/ramp down. 36" or wider is more than adequate for a side door.
5) Interior lighting: Go ahead and spend the extra bucks to have additional lighting placed inside the trailer and have a switch placed inside the side door. When traveling at night you will find this much easier than having to go inside the trailer and find the small overhead lights that have their own switch(es). 4' florescents work great but can be a bit more problematic with a low pro trailer if they're are not placed correctly.
6) Floor covering and interior siding: Makes for a much better looking trailer but be aware that floor covering can pull up easily and be cut by kickstands etc. I would NOT recommend putting normal floor coverings on the ramp as with just a little bit of moisture it will get slicker than deer guts on a door knob! Most part stores carry a 3M non-slip (sandpaper like) gritty self-adhesive tape. This combats the previous problem. Also, I know some that have used the spray in bedliners for their ramp and it works well also. If you don't want to get siding then painting your walls white will really improve the looks of the interior.
7) Get some E-track. It can be bought from your trailer dealer or if you're a DIY'er you can get it at Lowe's, etc. This allows for more functionality in tying down. While you're at it, check and make sure you're D-rings are thru the frame of the trailer and not just thru the 3/4" plywood. Have had D rings pull out before and I will guarantee you that will have you cussing and testing your religion!

Roof vents: Are a nice option but will leak if left open! LOL!
9) Although open trailers are preferred by many (mainly because of expense), any time I've had a bike on an open trailer and been traveling, staying overnights in motels are painful. Every little noise in the night will have you up peeking thru the curtains to see if someone is jacking with your bike. I HATE THAT!
10) Beaver tail: Get one if you plan on hauling a chopper or really low sitting bike. Hearing your frame and/or kickstand getting worn down and jacked up each time you pull in and out of the trailer gets a little annoying!
BUYER BEWARE: Not all enclosed trailers are alike nor do they even spec universally. Some mfg's count the V-nose in the overall length...... most more reputable companies don't count the V-nose (usually around 2'). Some mfg's place used tires on new trailers..... check 'em out. Some mfgs only put brakes on one axle..... get 'em on both. And check the axle mfg.... Dexter is kind of the industry standard and whether buying a single or tandem axle each axle needs to be a minimum of 3500lbs. Anything less on an enclosed trailer and I would feel like the mfg is trying to shortcut and would cause red flags.