So the terminator x max and cable is ~$1350 (when it's not on sale). (this is the one that has trans control). They also say skip the mini display if you're going to use a laptop, so I dunno if that lowers the price any or not.
That's the ecu and transmission control, fully done wiring harness, "an afternoon to install" kind of deal.
the pro evo with a harness is roughly 1800, the micro with a trans harness is 500, for the same kind of afternoon to install setup.
an ms3-x (which is what you'd want) assembled is 760, the unterminated harnesses for that are 85 each for 930ish. then you gotta buy new connectors or splice in old ones, in the correct order-not an afternoon
a microsquirt is 380 I think now, plus the connectors for the transmission, so even for the non-pro ms setup you're looking at $1310, and you still have to spend a while wiring everything up, etc.
seems like a no-brainer to me. You will get more features from an ms3 based system (more specifically, one of the pro offerings, not so much the metal box ms3-x). I'm not an MS hater by any stretch, don't get me wrong on this, but it's not nearly as cheap as it used to be.
You can probably get close to the cost of the terminator x max with an efi source gold box setup... looks like one with the tcu built in and both harnesses is around 1750 (which isn't all that bad either really)
As far as the hpt route, I can elaborate on that a bit as well, so if you don't already have a dongle, you're looking at $300 for the new one, plus probably $200 in credits to license the transmission and engine.. and that is if you get the basic dongle. the pro feature set adds another $250 on top of that (and you may or may not want any of that, you can get a wideband interface with an aem wideband I think, but otherwise you'll need the pro set iirc or hax to get wideband info into your datalogs.. and you will want that).
In terms of standalone harness costs.. most people I've seen that have such harnesses spend somewhere between 5 and 600 on them, I did have a guy that rolled his own the first time, and we spent 2 hours on the dyno tracking down broken wires and incorrect pinouts.. then he was out of gas, so he still had to pay for the full session and got nothing out of it. He was mad at me for a while after that but when the car finally came back after visiting another tuner, getting a new engine, new harness, etc... he was a lot happier with the results.
So realistically, the cost of an ls swap with the stock ecu and hp tuners is going to set the end user back ~$900-$1000, you can obviously trade your time for money on that deal far better than you can with any of the other options, but the time cost for a first timer is going to be significant, esp if it's a gen4 and you're envisioning big cam type stuff.
If you're going to do a mild cam stock intake/tb type setup, it's not bad. Once you get the scanner configured it takes on average half a dozen to a dozen WOT trips to get the maf curve dialed in. You won't be able to trust the knock sensors really anymore with a cam swap, but that'd still be your best bet on a mild setup to get the timing around where it wants to be. On gen4 stuff, jumping into virtual VE tuning is crazy, apparently the best thing to do there is patch the OS and use hpt's normal VE table.. that you'll have to either find someone's or generate an entire map from thin air the first time. I usually do the t00ner thing and flip over to pure MAF, I haven't had any issues with that to date.
The things that are absolutely critical to a good result with the stock ecu are injector data (all of it, not just low pulse numbers and overall flow rates, those are important too), it has tables of offsets that are bigger than most VE maps, and if that information isn't good, you will spend hours trying to get the vehicle to idle right and cruise down the road without doing stupid ****.
I would say Gen3 stuff is my favorite, it's not overly complex beyond the setup information (injector data, etc) and has real time tuning offerings and such. I can usually get a gen3 setup to about 95% map and maf in about 9 or 10 pulls, and then it's another hour or two playing with the timing maps and modifier maps to get things nice.
To date I have only had one or two gen4 vehicles that took me less than about 3 hours to get dialed in on the rollers, they have just... a ton more modifiers and modifiers for modifications, and once you start to get your head wrapped around it it's kinda mind boggling. The Gen5 stuff is apparently even crazier, I think I'm just gonna skip that and outsource it.