Holy fucking shit. First of all, I'm incredibly jealous. I can't even put it into words. $2k is way out of my price range for the foreseeable future, and I really want some custom boots.
As for the design itself, I have no idea what you like, but I can say what I'd do and why, so maybe that'll be helpful.
I like nice boots, but not really flashy ones, so personally boots with a lot of weird colors are a non-option. I'm not a West Texas hippie, and I don't get my idea of "Western Attire" from John Wayne movies, so it just isn't my thing. Similarly, unless it's a Texas theme or something, I don't want pictures on my boots, which eliminates a lot of their pre-made options. The reason for this is simply that I can't guarantee that I'll find the same image to be as appealing years down the road, and I want my boots to be wearable for a long time—so I will say I kinda agree with your girlfriend on that point. That said, I do like detailed stitching and hand-tooling, so those are the part of the site I'm looking most closely at: Hand-Tooled and Simplicity, as well as Men's Club.
Before thinking about decorations though, you first need to decide what kind of boot you want. For example, I hate roper heels, so I'd make sure to get a Riding Heel (or Walking if they don't have both, but it looks like they do). Additionally, I know fat fucking square toes are "in" right now (and I do own a pair), but I don't like em and seriously doubt they'll be here too much longer. Plus they make your feet look huge. So I'd go with either a traditional tapered toe or the somewhat-snipped toe that seems more prevalent on the site, that's preferential. On top of all that, I like tall shafts on my boots, so I'd be looking for something like 13" instead of the common 11. However, changes like these (at least the shaft height) may add some to the price, so that'd cut down on other customization you could do for the money.
That still should leave you with ≈$800 or so of leeway though. So then you'd look at what kind of leather you want. Obviously, like you said, exotics like croc are going to be out of your price range, but alligator could be an option, as well as ostrich (if they even do ostrich), elephant, or suede. Now that'd probably be only on the foot part, not the shaft, but you could probably squeeze one of those in there for the price.
However, if you didn't want to do that, you can stick with standard leather and add some flash to the rest of the boot in the form of tooling, stitching, or color. Color is the most noticeable, so if you have a favorite color that you think you'll stick with for the next few decades, then by all means throw that on there if you're so inclined. Personally, I'd opt for tooling; from the site the "Tularosa Cowboy" or basically any of the intricate, mostly-brown/tan boots in the hand-tooled section are good looking designs, and I don't have the creativity to come up with one completely on my own so I'd tell them to have at it. If you have a bit more artistic flair, then giving them some idea of what you're thinking would be a better bet.
Beyond that it all comes down to you, and I know this is a rambling mess but it's 5am so feel free to completely ignore it lol. I guess tl;dr: Start with the specs of the boot itself, weigh your preference toward exotic or flash, and don't pick something you'll find tacky in 20 years.
Just so you get an idea of what I like from their site, here are some designs I would wear or start from, in no particular order: (and yes some are women's but I'm just saying I like the style)