HPTuners is pretty decent and can do most normal changes that people will want in a tuned car. The best parts about HPTuners it is the built in scanner and the programmable histograms. For example, since I am running Open Loop 100% of the time and have my wideband connected to the fuel tank pressure input at the ECM. I programmed a few histograms to display the actual wideband A/F ratio average for every cell on the MAF as well as a VE table any time I log the data. It also has one that compares the actual wideband A/F ratio with the commanded from the ECM and logs the average error %. This error % can just be copied/pasted from the scanner screen to the editor screen to change your MAF calibration to dial the two in closer. It also has filters, so mine are setup to ignore any data where the engine is delivering less than 15 lb-ft (off throttle/decel). Like I said, the scanner/histograms are the best part about HPT.
HPTuners (and most current tuning packages) use credits or some other means of limiting the application of the tool to multiple cars without some exchange of additional $$$. HPT comes with 8 credits and will allow you to program 4 or more cars. The PCM/ECM/TCM is 1 credit per component, so the late model stuff with ECM/TCM combos = 2 credits per car = $100 (there are other options for more unlimited use, but those are not cheap either).
HPTuners does not have built in virtual VE tables so you have to use the 3rd party BlueCat conversion tool, or buy a custom OS from HPT to get a VE table with the Gen 4 ECM's. EFI Live has a built in Virtual VE tables. The V8's (and probably anything with variable valve timing) use what is called dynamic fueling where it runs both Speed Density and MAF up to 4000 rpm (or wherever you set it) and 100% MAF from 4000 to redline. The SD side controls the transient fueling, so you get the best overall performance when you tune both SD and MAF, but there are many guys who run 100% MAF and never touch the VE side of things, as well as those who run 100% SD - I prefer to tune both and keep both active.
HPTuners will allow you to do segment swaps (like mixing/matching transmission code and engine calibration), but you have to send your ECM into them to do it. EFI Live and TunerCat allow the end user to perform segment swaps.
On the E67 LS4 calibration, HPTuners does not have access to the vast majority of the transmission DTC. So if you do a manual swap with an E67 LS4 (and possibly some other applications), you will have to get someone with another tuning software to turn off the transmission DTC (I had Darth do this with Tuner Cat).
On the 58X ecms HP tuners is missing some O2 sensor transport delay features that other packages have. This becomes important with large overlap camshafts and moving the O2 sensor further from the engine (like with a header install). This is part of the reason I run 100% open loop. I had the STFT dialed in under 1% variation and could feel when the O2 sensor switched rich/lean - and subsequently adding/removing fuel - in town and on the interstate. The constant pulsing irritated me. The pulsing goes away open loop.
As you can see, I don't think HPTuners is the perfect tuning package. I am glad I have it, think it is worth the investment, and really like some of its features, but there are some that I now know it is lacking (but I also think that every tuning package is lacking something). I think for someone looking to get into tuning professionally across multiple platforms and including vehicles 2007+, you need access to multiple tuning packages.
Now about BCM's and late model ecms... The E67 ecm doesn't "need" the BCM to run the engine (at least with the V8's). All I did was disconnect it and turn off the DTC for it. However, there are some built in features within the E67 ECM that will only work with the BCM connected. The reason for this is the brake position sensor input goes to the BCM - its status is communicated through the CAN wires to the ECM, not the ECM. So without the BCM, the brake position sensor is "gone". Without the brake position sensor, you will not be able to perform a CASE learn (brake pedal must be pressed to initialize), electronic cruise will not work (must be able to turn off when brake is pressed), and DoD will not work (same reason as cruise), and there may be some other things.
[This message has been edited by fieroguru (edited 09-02-2013).]