to do the haltech you can have the stock ecu flashed by technosquare for what's called a tuner flash, think it's in the $300 range I believe, & this will give you everything you need without an uprev flash to the ecu. the haltech is more expensive initially, but consider that it has built in boost control that may approach 4-500 for equivalent control electronically, & also consider that it has built in ability to control alcohol injection which would also save you about as much as your saving for the boost control, & also consider that it includes awesome data logging ability which can go a long way toward getting a great tune, all this added up can kind of soften the blow of the initial sticker shock.
the haltech is better than the stock ecu option for a lot of reasons, but that don't mean that the stock ecu is a horrible idea either really... just weigh all the add'l costs that the haltech can save by having all control in one interface & by one unit that is boost aware & the data logging abilities & the gap does narrow a bit... in the end you should probably go with the tuner you feel most confident with & go with what he feels is the best option... opinions can vary & there is more than one way to do something like this for sure... there is no right & wrong, just different opinions on what's better & what's good enough...
also consider that the haltech is wide band compatible & boost aware meaning maps can be built depending on boost levels, the haltech will offer more precise tunabilty for a FI setup in my opinion. inspection & legality issues I'm surprised that he even used this as one reason because the same thing would be doable with the haltech anyway... the haltech retains the stock ecu & works with it, & a good tuner can take advantage of the stock ecu maps in the region they apply to even with a haltech...
---------- Post added at 02:22 PM ---------- Previous post was at 02:08 PM ----------
also, just to also point out for consideration, in using the haltech you really should also use there external map sensor which is just under 100 I believe, & then you really should add there dual wide band add on which is ~$400 I believe... you will def want a wide band anyway, but the benefit of the haltech dual WB is that #1 it can be used for more precise closed loop operation & most importantly, it's data can also be logged along with every other perameter... don't dismiss data logging ability. that can help smooth out any anomalies you may discover in drivability after the tune, where without data logging your tuner would then have to recreate the condition you speak of & try to see it to react with tune compensation. dyno tuning can only do so much for drivabilty issues