I'm fine with players becoming highly skilled after all there is a need for death squads as well as spys.

Indeed, if it was up to me to design DH2e, characters wouldn't grow much at all beyond the baseline in terms of personal ability. But then, to me DH isn't the sort of game where there's any reason PCs should end up being able to out-melee a Khorne Berserker.

I can see where you're coming from, but in this case I'd recommend actually splitting DH into two different games - one for "street level" characters, for groups composed of hiver thugs and IG conscripts, and one for the actual TT-style Inquisitors and their highly specialised retinue of professional Assassins, Psykers, Battle Sisters, Space Marines. There's lots of styles of investigation and combat for both, but shoehorning archetypes from the former into a low-power game would be very awkward indeed, either ending up with broken balance or seriously nerfed portrayals.

Personally, the Inquisition has never been about "low power" for me; I'm too familiar with GW's material to really buy into all the "lowlife scrub acolyte" stuff - so whilst I would enjoy a "low power" game in this product series, I'd rather have that be about something like, say, gang warfare in a hive, a la Necromunda. Shadowrun meets 40k, so to say.

If we want a this we need some way to stop Minmaxing with xp. I recommend a tier system with Tier 1 being DH1/OW starting level, when players reach the level where they should be Tier 2 they can buy a Tier 2 package they meet the prerequisites for which can give stuff like True Faith, more aptitudes or anything else that fits. I see Tier 2 as veteran storm troopers, Sisters of battle, IG Captains and other elite individuals and Tier 3 as Inquisitors and other Peers of the Imperium.
On a side note would anyone object to having Fate Points rolled at the start of each session (d5+/-homeworld) and each tier giving +1 to the role? I know we would need a new way to cheat death but it would mean that thee one player to get a 10 or a 1 on their roll would not have that for the whole campaign and temporary Fate Points could be given out for stuff like killing a Master.

I'd rather just make everyone start with three fate points and avoid rolling entirely.

Interestingly, there is a talent in version 2 that allows you to sub Fel for requisition tests.