Weird. Maybe it's just because of how the smog laws work here in California (you have to swap EVERYTHING emissions related from the donor to the recipient in order to be legal, including the ECU), but when we do swaps out here, we always just assume you'll swap the ECU and entire wiring harness. It's not a big deal if you just do it all together. Some guys go through the trouble of separating the unused stuff from the loom, some don't. And guys out here are putting LS engines into EVERYTHING. LS-powered Jeeps, meh - We got LS-powered Miatas and RX-7s. The first time you see one of those, it gets your attention.
It isn't the smog laws, its the basic operation of every feature of the new JK's. Without the Chrysler/Jeep ECU even the radio controls don't work, let alone door locks, ESP (Electronic Stability Program,) antilocks, TPM (Tire Pressure Monitoring,) etc. The Chrysler/Jeep system is incompatable with the GM system, so there is no integration, no add on that works that I have read about, and I look for this stuff.
Even getting the Hemi to work seemlessly has been a challenge not every would be converter has mastered and that is but one reason picking a good conversion kit is important. For that matter installing some of the lower end lifts can be fraught with ECU challenges, with the dash board lighting up like a Christmas tree, the ECU throwing codes and the ESP kicking on.
As far as smog laws go, California has the tightest. MD has followed California's lead, but when the tester is plugged into the OBD port the AEV Hemi conversions will pass.
BTW, federal regs require an engine of the same year or newer be installed for swaps.
I have a 6.0L powered Suburban. The Hemi is every bit the equal, really more, though .3L smaller. Where GM shines and Chrysler/Jeep doesn't is in auto transmission programing. The auto in my Suburban is always in the correct gear and when it shifts up or down you know why and it does it at the right time. Once in a while the Chrysler transmission programming will leave you wondering why it up or down shifted. But that happens infrequently and it isn't a big deal.
I love my Jeep with the 5.7 VVT in it and if it was totaled tomorrow I'd be back on the phone with AEV for another 5.7 VVT.
BTW, I've driven an AEV 6.1 Hemi powered Jeep. All AEV Hemis are autos with the 545rfe and mine runs on 37's with 4.88's, that Jeep was on 35's with 4.88's so you would expect more performance just because of the smaller tires, but the difference was pretty significant. That one had enough to burn the 35's from a dead stop, no wind up just hit the petal, at least until the ESP program caught up and dropped revs.
On the other hand, the one fellow who I know has had both the 5.7 VVT and the 6.1 hated the 6.1 and loved the 5.7 VVT. AEV recommends the 5.7 VVT and told me that the 6.1 has a flat spot right where you wouldn't want one and didn't produce the torque down low that the 5.7 VVT does. I only drove the 6.1 for maybe fifteen minutes and only on the road but I didn't notice the shortcomings. The 6.4 is also a VVT engine and is supposed to have the same torque and HP curves as the 5.7 VVT but just more, lots more. The 5.7 VVT is plenty enough. {Edit to add that EVERY Hemi has more torque at 1200rpms than the oem 3.8L puts out at max, which is what makes them so fun to drive.}
My wife has an auto '08 JK Unlimited Rubicon with only a 2.5" BB on it, so the oem 4.10's and 32's along with the 3.8L. The 3.8 power is ok, but the 42rfe four speed is not a good match with too steep a jump from 3rd to 4th. The forthcoming '12+ 3.6L which puts out that 88 extra HP and 60lbs' more torque will be mated to the 545rfe, which has the same 1:1 3rd ratio and nearly the same top O/D ratio as the 42rfe but has its fourth gear right between the 42rfe's third and top gear, which makes highway down shifts drama free - and the Hemi makes them less frequent to begin with. So, with the new five speed and the extra power the 3.6 offers, the 2012 JK's might just make Hemi swaps more rare.
JPK