Money is certainly one of them. It's not exactly a cheap hobby, even though I do a lot of DIY. I use cheap pots made from recycled plastic. I make my own nutrients. I use tap water and make use of its constituents. But the pumps, pH/cond-meter, wind screens, racks and fittings are expensive, and sometimes I wonder why on earth am I doing this?
The answer is . . . I just LOVE it.

That's the truth - money is definitely something most people underestimate when they start looking into hydroponic gardening.

Usually there's a pretty good opportunity for starting small and relatively cheap and building up from there. But personally I'd rather spend a little money and get a really good quality hydroponic nutrient. With hydroponics it's too easy to end up with a ton of problems in your garden really fast if things aren't formulated right and I just don't trust myself to do it that well.

I've been really happy with my switch to Advanced Nutrients products, which is probably why I lean towards thinking that the nutrients are what people overlook most often. I tried to cut corners there at first and it was just a disaster. I overlooked the importance of good nutrients and it really showed.

I have a 24 x 24 ebb and flow with a 10 gallon tank. I recently decided that I have been overlooking the importance of providing the most oxygen to my water as possible. I've always had a small air stone with a small air pump. But I've moved up to a $75.00 air pump and 4 - 4" airstones. My nutrient tank rumbles like a hot tub, now. I'm sure it's overkill but you can't have too much oxygen in the water and it helps keep the water agitated. That's what I've been overlooking.

For me, implementing a means to easily drain and refill the systems have traditionally be underestimated.
Even my systems this year had/have flaws. I remembered to put in drain plugs, but they're so close to the ground I have to use a pump to get them in a bucket. also, getting the nutrients and water back in requires a similar contrivance.
I tried to limit the number of openings into the system but that left me without a good way to stir things. I remedied this by premixing in buckets before putting into the system but it was a bit tedious.

You probably solved most this already, but one thing you could do with your draining/filling is to attach a bit of hose to the drain so you can open the valve and it will go up and into whatever you're draining into (as long as the fluid level in the waste bucket is lower than the reservoir).

You could probably do the reverse to refill, but that'd be a bit more complicated.

Alternately since you've got a pump it might just be easier to build a little PVC manifold with some valves so you can use the same pump to drain or fill any of your reservoirs without disconnecting and reconnecting stuff. Sort of a mini-version of what the commercial places use.

Lots of good answers here.

I'd have to say the most overlooked piece of hydro gear is QUALITY nutrient testing equipment (pH and EC).

I'm McGyver when it comes to DIY, but you just can't build testing gear like you can the other stuff.

That's my 2-cent's worth!
:O)

I think the one thing I overlooked personally (and have since fixed) is purchasing a TDS and PH meter - these are fairly invaluable but not a lot of guides discuss their use.

That's true, and along that vein is the proper pH adjusters. There's a lot of stuff you can use as a substitute, but a true hydroponic pH up or pH down makes a huge difference.

I didn't realize just how much until I traded in the cheapo thing I got to start with for the pH Up/Down that Advanced Nutrients makes.

Now when I adjust the pH it pretty much just stays stuck there. Before it seemed like I was always fighting to get it back down or up. It'd change, then change back.