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This is something I've been thinking about on and off for a while, decided to finally write it up. I've never done custom/homebrew rules before so probably gonna screw up quite a bit, just please be gentle when pointing it out.
General idea is that since they're such an elite army to go a similar route as Grey Knights. Since the GKs are generally "Space Marines+" I thought it would likely be appropriate for the Deathwatch to be "Space Marines++". For one thing going by the whole "elite and specialized strike force" thing, decided it would be appropriate to "Sternguard-ify" most of the units by giving squads free reign over the appropriate gear tables along with Special Ammo by default for Bolt Weapons (so Sternguard/Banguard/Company Vets won't be here because they'd be redundant) and raising stats (having BS5/WS5 as the standard for one, not sure about any others, but raising Wounds would probably be a mistake) with an appropriate increase in price along with making all Sergeants into Veteran Sergeants by default, also it would seem to make stuff like tanks inappropriate for them so for vehicles they'd just get Bikes, Dreadnoughts, Drop Pods and probably Land Speeders (though I don't really know what to do with those so I'll leave 'em out for now). Also, some Chapter specific would probably be appropriate to feature but not absolutely sure what Chapter-specific stuff or how. Also unsure about Centurions.
Speaking of Chapters, think it'd be best to leave their "home chapter" as a purely painting and fluff-related choice.
As far as Warlord Traits or anything, thought it would be a fixed Preferred Enemy:<Xenos Codex of your choice> for everyone in the Detachment but that might be better as a USR tacked onto everyone here instead with different Warlord Traits available (don't know what they'd be, though).
Now I'll get onto the unit ideas I thought of!

HQ:
Probably will have the Librarian, Captain, Chaplain and Techmarine in basically the same sort of role with the same sort of options (though it strikes me that the Techmarine would be a lot worse here without tanks and stuff to fix, mostly including him because the FFG RPG does). Company Masters, Chapter Masters, named characters and such really probably shouldn't be here.
Also would seem fitting to have an Ordo Xenos Inquisitor, but they might need to be decked out differently to fit in with Marines (like forcing some upgrades as default gear).
This Codex should probably have its own list of Relics and such, probably each being tailored to fighting a particular Alien race, at least thematically/fluff-wise.

Troops:
Tactical Marines: Sergeant would have basically the same options. Each guy gets to take a Special Weapon, one can take a Heavy Weapon instead (though most of them would be a lot less impressive in this configuration).
Scouts (not sure if they should be here but listed them because I have ideas): Would probably have some sort of variant on the Sniper Rifle as a standard weapon, not sure how to boost it. Thought of higher AP; a better To Wound roll, though it would have to stop at 3+ because 2+ against anything would be dangerously close to the D and strictly better than Strength 10; special rules of some sort, probably ones for special effects or maybe stuff like Shred/Rending and ID on 6+ To Wound (though that's probably too much). Honesty not sure how to make it better without going overboard. One can take a Heavy Weapon, anyone can replace their Sniper Rifle with a Melee Weapon. Probably would be good to give them some special rules for extra Scouting shenanigans.

Elites:
Terminators: Each one gets to pick from the Terminator Weapons table. They can also replace the Storm Bolters with Special Weapons instead of just the Combis or melee weapons on that table (they'd probably be added onto that Table at a different cost). Still one Terminator Heavy Weapon per five dudes.
Dreadnoughts: Probably the same for the most part. Not sure whether to make them all Venerable with the same statline or to make normal ones BS5/WS5 and Venerables BS6/WS6.
Ironclad Dreadnought: Also probably the same, excepting for any applicable stat boosts.

Fast Attack:
Assault Marines: Probably best to make them BS4/WS5. Sergeant's the same again. Each one can replace there Bolt Pistol with a Pistol of their choice (including the Hand Flamer) and their Chainsword with a Melee Weapon of their choice. In addition two can swap both weapons for a Special Weapon and one can swap both for an Eviscerator or Thunder Hammer (priced to balance against Pistol/Power Fist action. They're giving up a Pistol shot for a rule tacked onto basically the same weapon). Can of course be given Jump Packs or a Drop Pod, same deal as in the newest version.
Bike Squad: Sergeant's probably the same, but might want to give him extra options. Each other gets to take a Special Weapon and replace their Bolt Pistol/Chainsword with a Melee Weapon. Can attach an Attack Bike (and maybe a Land Speeder if they're included?). Might give them Skilled Rider and a rule with an effect similar to Ravenwing, but not sure.
Attack Bike: Can attach one to the above, or take a lone squad of up to three. Aside from stat boosts, mostly the same except that they can take a Heavy Weapon (not just a Heavy Bolter or Multi-Melta, though the latter is still probably the best option).

Heavy Support:
Devastator Marines: Probably best to make them BS5/WS4. Sergeant might be the same, but maybe he'll get the option to swap both weapons for a Heavy Weapon. Each can take a Heavy Weapon (so aside from stat boosts, the only real difference is letting the extra 5 Marines get in on the Heavy Weapons fun).

Lords of War:
Don't know of any that would fit since most Space Marine Lord of War units are special named characters or Super Heavy vehicle, neither of which really fit.
Though maybe they could be left open to the Forge World options anyway (making the one Fellblade/Spartan/Thunderhawk/whatever the only real vehicle in the whole detachment), though that could be a bit odd.

Fortifications:
Not sure about the normal ones, but maybe they could have unique portable Sentry Gun-type things. Probably could be repaired and boosted by the Techmarine and his Servitors, who would also be needed to move them during battle (mostly so the Techmarine wouldn't be an auto-avoid).

Not sure what kind of Formations they would get, if any. Maybe fluffy ones that combine them with Inquisition units under an Ordo Xenos Inquisitor, small specialist ones, or maybe ones that stuff Deathwatch units into an actual Space Marine detachment with otherwise normal stuff.

Tactically these could be a bit OP with the boosted stats and hordes of fancy stuff, but simply high stats and good equipment wouldn't be too much of a problem (just price it up and it's a case of "you get what you pay for and you paid a lot") and with low model count that are still just Marines you could counter them with the typical Plasma/Melta/Lascannon/just drowning them in saves (plus Grav Weapons would utterly eat them alive!), which is the main reason I insisted on no extra Wounds (better Saves would be really iffy too unless they're really minor stuff).
The REAL "unbalancing factor" would be how you don't have to take "filler" units, whereas with a normal Tactical Squad you could have Plasma/Melta/whatever stuff for anti-armor the rest of them would be stuck with unsuitable Bolters while here they could ALL have weapons that fit their role and you don't have to "waste space" with Boltgun guys. So there'd need to be a further increase in points as a "this is for not having to have basic weapons" tax.

But unless they end up broken they'd probably be an "ally army" like the Inquisition, Imperial Knights, AdMech, Tempestus and so on.

P.S. Sorry again if it's badly written, full of bad ideas, etc.