Retire obsolete SAM's, get rid of SA-2, 3 and 5. Push for production of SA-10 as the main army missile with the SA-12 being for fixed defences. SA-8 and SA-6 to be upgraded as much as possible but also work on replacements.
Actually, SA-12 is the Army's SAM(SA-4 replacement), while the SA-10 is PVO(SA-2/SA-5 replacement). SA-11 replaces SA-6(as well as SA-3), while 2S6 Tunguska seems to be the SA-8 replacement.
Navy.
Submarine force.
SSBN's
Delta I and II - retired and scrapped.
Yankee - Retired and scrapped.
Delta III - consider conversion into SSGN cruise missile sub.
Delta IV - repeat production
Typhoon - Halt construction at 6.
Delta IIIs would be poor SSGNs, big and noisy. I suppose if you want strategic cruise missile boats, you can:
1) Convert Yankees(one or two were converted to fire SS-NX-24);
2) Build an Oscar variant(don't know how desirable it would be to blur the line between tactical and strategical units in this case);
3) Build a new class(Soviets had a few SSGN projects that weren't built; one of them was bigger than Oscar, and I think Delta III);
4) Use Akula in the role(I think that was the Soviet Navy's idea; the Akulas have 6 SS-N-21 tubes after all, and no other contemporary Soviet SSN class had these tubes).
Typhoon is too big and expensive, but I think the Soviets would build 7(one submarine squadron), and have the Delta IVs replace all other SSBNs.
SSN's
November - retire and scrap.
Alfa - Retire and scrap - far too unreliable and unsafe.
Victor I - retire and scrap
Victor II - begin phased withdrawl and scrapping.
Victor III - retain.
Akula - Concentrate production to make mainline submarine, when one comissions, remove a Victor II.
Sierra class - cancel construction to focus on Akula class.
Agree with Alfa, November and Victor fates. I think the Soviets would go for a Sierra/Mike mix as their new SSNs, with the Akulas being used more in a SSGN role, as said before.
SSGN's
Echo - retire and scrap
Charlie 1 - retire and scrap.
Charlie II - Retain until replaced by..
Oscar - Upgrade all Oscar to Oscar II standard - continue to produce to replace older SSGNs.
SSK's
Whiskey - Retire and scrap
Romeo - See above
Foxtrot - see above
Tango - Retain as training boats
Kilo - continue production and see what the hull can be improved to do. Push for exports market.
Agree with all of these.
Surface ships.
Kiev Class - Modernise and upgrade to same standards as the Admiral Gorshikov.
Moskva class - scrap/sell.
Ulyanovsk - prioritise for completion.
Kirov class - Modernise and upgrade
Slava class - continue production and look into making a multi-role cruiser
Kynda, Kresta I and II - scrap.
Kara - modernise and update weapons/sensors.
Begin design of a AA cruiser/GP cruiser hull for fleet defence.
Sverdlov - scrap/museiums.
I'm not so sure the Admiral Gorshkov/Vikramaditiya conversion is a good thing, but converting them to the Baku standard would, if possible, be better.
Agreed on Moskva, Ulyanovsk. Agree on Kirov, and I'd say one more unit(in addition to OTL Petr Veliky).
Slava... don't like that design much, but there are a few projects to upgrade them. Scrap Sverdlov, Kynda and Kresta I. Kresta II might still have some use, or could be sold to foreign navies. There are some
very interesting upgrade projects for Kara that could be used, to keep them as the major Black Sea units.
As for an AA/GP cruiser project, search for "Project 1199 Anchar".
Skoryy, Kotlin, Kidlin, Krupny, Kanin - Scrap they are utterly obsolete.
Kashin - Upgrade to Kashin II at least.
Sovremenny/Udaloy - Continue production.
Krivak class - Begin modernisation of Krivak I and II to Krivak IV standards, retain Krivak III, look at what the hull could be developed into.
Grisha - Modernise.
Riga, Petya, Mirka, Koni - Gone
This is just off the top of my head..there's a lot to be done. The massed disarmament would calm western fears, save money and possibly lead to a more professional armed forces for the Soviet Union.
Agree on scrapping anything earlier than Kashin. Not sure I'd upgrade Kashin, would try to replace them with something like the Project 1135.6(the Indian Krivak frigates), or the Admiral Makarov standard that's currently being built for the Russian Navy. Keep building Sovremenny and Udaloy, but look for some development of Project 21956 as a common successor of those classes.
Not sure Krivak I and II can be upgraded to Krivak IV standard. Also, remember Krivak III are Border Guard(KGB) units. The Krivak IV would be the main Baltic/Black sea unit, together with Project 1166 Gepard, which would replace the older SKR/MPK/MRK.
One last note; a professional military would go against Soviet dogma, as I understand it. Even now, there is strong opposition to a professional military in the Russian Armed Forces, for many reasons.