What medium should I use to connect my water heater?

I would go with the regular copper, soldering the connections is relatively easy. You can practice with some scrap/left over pieces if necessary. Just make sure you clean the outside of the pipe and the inside of the fitting well, apply the proper flux and use solid, lead-free solder. Heat the fitting over where the pipe is inside it and the solder will wick right in. Also, make sure no water is trickling through the line when trying to solder. Sometimes you need some coat hanger wire to support the parts while soldering them.

If you are really woried about your soldering ability, and you don't have a friend that might do the work for beer, they also have these copper fittings that you don't solder, they have an O-ring in each end, you press the pipe in each end and crimp them with a special tool, these are good for situations where you you can't get the water completely shut off, or places where trying to use a torch might present a greater than usual fire risk. It might be possible to rent the crimping tool.

Added:

If the rest of your hot water supply pipes are 1/2", then you can use 1/2 for these connections. If the pipes leading in/out of the tank are 3/4", as they often are nowadays, it would be better to use the matching size (even if you have to buy a few parts) so you don't impede the flow. As for the 45 degree elbows, sometimes you can these instead of 90 degree elbows to cut down on the number of sharp turns in the line, it depends on the particular configuration you need and your imagination. They also have large-radius 90 degree elbows (sometimes called "easy ells") which also work pretty good.

Beaver, if you're the least bit uncertain about your soldering ability then there are a couple of other ways you can go. One is the new connecting fittings with teeth, I think they're called Sharkbite fittings. They have little teeth inside the fitting plus an "O" ring to seal the connection. The teeth lean in, which means once the pipe is in the fitting it's not coming out. I've never check prices on these things as I learned to solder copper pipe when I was 10, so have never needed them. But they say they work just fine for folks that don't do this stuff all the time. As for the 45's and 90's, I'll leave that to you to design. The difficulty level on this one should be low, if you can measure and cut pipe, then you should be able to press it into the fitting.

We use copper flex as they are easier to fit and sometimes the heaters need to be tweaked or moved a bit for the vents to fit right . The nylon are acceptable by code and shouldn't have a bacterial issue .The PEX , well some PEX manufacturers require a foot or so while others say it is safe to connect directly to the heater . Here the city code says 2 feet of copper or brass pipe so the copper flex works fine . plus the flex lines give a dielectric brake and much easier for future replacement of the heater as you don't have to cut and solder again

unless this is a small under sink heater you need to use 3/4 supply and out let next you should be able to get in to work with less 90s remember you can turn a 90 to a 45degree angle and last thing use dio electric union on the lines not the nipples they dont work and never run pex right out of a water heater stay at least 1 foot away with pex

The only issue I see is that you can also build deposits and bacteria in the copper flex. I would use ridgid copper with as few elbows as you can. Try and use some 45's rather than a 90 to make a smoother transition.

I just built a new home with 100% pex and LOVE IT!