The things that bother me most is that there's no way to measure throughput directly. You can measure the rate at which a storage tank fills and depletes, that's the closest you can get. But that can be very unreliable.
Pipes slow down throughput by a lot but it's so freaking hard to tell by how much. There's nowhere you can put your cursor and see, "this pipe is transferring 'x' L/s", can't do it for pumps either which would make the most sense to me.
But fucking fluid wagons. My god. Either fluid wagons or barrels need a balancing pass, because it just makes no sense. I'm making my entire rail network out of 1-2 trains, and basically trying to find the absolute maximum number of 1-2 cars I can cram down a rail before the rail itself becomes the bottleneck. So it's critical to keep the same acceleration characteristics for every train on the network. If I want a fluid wagon to have the same acceleration as my 1-2 cargos, I have to put three locos on the front. That's just so insane! It takes a 3-2 train to match the speed of a 1-2 cargo wagon... but then check this out.
A cargo wagon full of barrels holds 100kL of fluid. A fluid wagon holds 75kL. So the cargo wagon beats the fluid wagon on capacity too, by a very significant amount. A barrel of fluid weighs 1/8th of what it does in a fluid wagon.
Lets move on from the train characteristics. "Isn't barreling pretty cumbersome compared to just hooking up a pump to a fluid wagon," you might ask?
Only marginally. Look at this setup. 4 Unloads a full train of barrels at almost the same rate as a fluid pump can unload a tanker. And those chests that they unload to hold 48 stacks of barrels each, which is equivalent to 4.8 storage tanks. So this unloading station is functionally equivalent to a pump with 19 storage tanks hooked up to it, without the flow rate problems that you run into transferring from tank to tank. The only downsides being higher investment for the speed mods (likely not even necessary in lower tier tech factories) and power for the assemblers.