My biggest complaints about the SA client after having used it now for a few months, primarily with tamer characters and a little bit of crafting but no PvP, are:
(1) I can't ever seem to find a good zoom level while I'm out hunting. I have to zoom in close to make sure that if I have to take a few steps to keep vetting a pet, I don't "overshoot" my destination by walking too far. However, when I zoom in like that, I don't feel like I'm seeing all that I should be able to see headed in my character's direction. As a result, I usually can't hunt for too long in SA before feeling completely drained from messing wih the zoom level or trying to pay extra attention to sounds and scrolling for new potential targets that aren't yet close enough to see.
(2) Tooltip information isn't dynamic. For example, if you insure an item and have the tooltip info up, the tooltip box of text doesn't add the "Insured" tag. You have to mouse over the object again to see the new information.
(3) Blood tiles that spawn when killing something and that disappear too slowly, so that they interfere with being able to loot corpses. It's annoying to have to click past 3-4 blood tile objects almost every time you try to loot certain types of monsters.
(4) The atlas isn't resizable, doesn't show other character locations on it, and the circular map view is too small. I love how you can zoom in and out and can easily pull up maps of other locations, however. But it certainly isn't a very good replacement for UO AutoMap.
(5) I miss the UOAssist Organize agent for automatically moving all objects of a certain type into a specific container in your backpack (e.g., moving a bunch of blank runes you just bought into a bag before you go out on a rune-marking trip). I also miss the UO Assist Sell Agent. I use it fairly often when training up a carpenter or tinker to sell the objects they've made to an NPC to get them out of my backpack and make a small amount of gold while training.
(6) I also haven't figured out yet how you bring up a list of everyone that you're partied with, i.e., the "party manifest."
(7) I hate having to run UO as a fullscreen application so that I can't see the Windows Taskbar. However, SA runs terribly for me if I don't set it up to run fullscreen.
(8) There is no option available to follow a monster, character, or NPC. This makes taming stuff more cumbersome especially if your zoom level isn't set just right (see "overshooting the destination" comments above). It is also a feature that I will miss when doing peerless like Lady Mel when you want your pet to "follow" the monster it's killing even if the monster keeps hiding itself all the time.
(9) I miss seeing my character's health bar edged in red while in war mode.
(10) I hate having to rename pets before releasing them with a command because there's too much risk of releasing the wrong pet if you use the context menu to release them.
(11) And last but not least, I truly hate the stance of the male paperdolls and the male human/elf faces. Almost all the other graphics I can overlook. I guess maybe its a blessing in disguise that I don't have room to leave the paperdoll open and fortunate that I don't have that many male characters. I am fairly pleased with the female paperdoll and the look of most pieces of armor on the human/elf female paperdolls. I do wish though that you had the option to show helmets as circlets on the elves.
There's nothing on this list of things that annoy me about SA that keep me from using it. But a lot of these things are just irritating enough to make me grit my teeth sometimes at the thought of logging into UO while using SA. It always feels like a relief to log into the old, comfortable 2d client with UO Assist.