Therein lies I think one of the bigger issues with regards to pve endgame.
The way gear is acquired overall vs. what gear can be obtained in what content pretty much eliminates the value of a huge portion of the game's content.
Regular level 50ish instances-- No real purpose when a few BM/recruit pieces and some orange pieces with daily comm armorings and GTN snagged level 49 purple mods/enhancements outpace anything to be acquired.
Hardmode Flashpoints-- The ease of entry into storymode ops in conjunction with augmented BM gear means that you pretty much skip over the tionese +partial columi stage entirely. A few columi drops might still be worthwhile but by and large once you've gotten your BH comms for the GF daily irrelevant again, this is exacerbated by how many columi comms it takes per pieces compared to alternate gearing means.
Lost Island-- To run you are generally pretty close to full columi+ already, rakata chest can be nice but otherwise you will basically outgear the drops again by the time you run this.
Storymode Ops-- Ease of entry for for KP and EV are nice to make it a good way to gear up fresh characters fast, but by making this tier 2 difficulty (i.e. on par with hardmode flashpoints) you negate most 4 man content (BH coms aside)
Hardmode EV/KP-- SM EC--WIth a war hero barrel/hilt and a few BH pieces the drops from here are going to look mighty mundane. Some value filling in remaining columi with rakata but should be a primary gearing method not "fill in whatever I don't have BH comms to finish up yet"
Nightmare mode-- Basically a pure "can we do it" test as there will be little in the upgrade department here once you are sufficiently geared to run it
The combination of being able to augment everything now, having Black Hole coms be gained through so many sources and yielding top-tier mods, and the capacity to be full BM with a couple WH pieces within a week or a tad more of hitting 50 all serve to allow the player to bypass most steps in PVE progression.
So what's the solution? Hard to say.
Is it fair to tune content to be reliant on gear already being augmented? This would result a lot of irritated people, but the problem is that when encounters are not tuned to those fully augmented then augmented gear serves as effectively a tier higher then it is, or allows someone in say fully augmented BM to be statistically on par with non-augmented Columi except with a sizeable boost to weapon damage and force/tech power.
What about how readily BH coms are acquired? Dial that back somehow? Perhaps make gear acquired this way on par with rakata instead to allow a greater purpose to campaign? Might work, who's to say?
Perhaps tweaking pvp gear to make it less viable in pve somehow? This would anger a lot of people as making enough of a dent such that it doesn't replace anything below rakata would both be an annoyance for pure pvpers wanting to knock out some dailies for coinage and cause the "casual" mass to bring up that whole "game only caters to those with too much free time" argument you already see when discussing min/maxing WH gear and such.
Perhaps the answer lies in what is acquired where-- Remove the separation of Tionese coms and crystals and make it com only, prices are adjusted accordingly such that you can obtain tionese gear about twice as fast, making it so tionese can be obtained while you still have some use for it (aside from an easy place to dump BH mods to retain the set bonus), daily comms can be traded for tionese at the 3:1 ratio used with pvp comm ugrading, columi costs are reduced by about 30% so that you are buying more than one piece before you've outgeared it with BH and a couple rakata pieces (but not so easily that it negates tionese), Rakata gear is dropped as it normally is dropped or on-par is obtained via group-finder and BH weekly-related commendations, the current black hole gear is gained via nightmare modes, and campaign gear is acquired from its traditional sources.
about making pvp gear and pve gear less viable.i agree. It should be even more differend and unusable. if u do wz gear pvp if u do pve gear up youre pve gear.simple as that.