I'm not a fan of such 'deckbuilding' in multiplayer. More experienced players should have enough of an advantage without potentially being able to pull things that a less experienced player may never have seen before, let alone have any idea how to counter.
On the whole, I think it's important for the 1v1 melee to remain in the game - it's an archetypical part of the franchise. However, I would also love for the chance to see fleet battles involving the different types of ships working together as well as the 1v1 (often rock-paper-scissorsish) dogfights. Imagine, for instance, a classical Alliance fleet - slower Cruisers and Broodhomes forming a firebase at the core, Terminators forming a cordon to block enemy fire with their shields that the Cruiser point-defence can't handle or diving on enemies that close with the fleet with their powerful close-range guns, Penetrators, Skiffs and Scouts dogfighting with their opposite numbers or harassing slower enemy ships, and X-Forms using their flexibility to act where it would help the most.
In single-player, this could be represented either as more of an RTS mode - or you could take control of a single ship to control as normal, with other allied ships responding to your actions according to the type of ship. For instance, using the SC2 ships as examples, you could have the following categories:
Capital ships: Large, powerful ships suited to being the core of a fleet. Cruisers and escorts will try to remain close to capital ships, protecting them from lighter enemy attacks while the capital ship's firepower destroys enemy ships. Examples: Avatar, Broodhome, Dreadnought, Marauder.
Cruisers: Slower ships that are lighter than capital ships, and are suited to flanking capital ships to defend against lighter enemies. Alternatively, where capital ships are not available, a cruiser or group of cruisers may serve as the core of a fleet, being protected and supported in turn by escorts. Examples: Cruiser, Intruder (would not have the warp-in attack in fleet battles), Jugger, Podship, Terminator, Trader.
Escorts: Light, fast ships whose characteristics make them well-suited to defending and supporting heavier ships like cruisers and capital ships. If no such ships exist, they may act as raiders, albeit more inclined to operate in squadrons than true raiders. Examples: Blade, Drone, Guardian, Penetrator, Stinger
Raiders: Light, fast (usually) ships whose characteristics make them unsuited to operating as part of a fleet. Such ships may retreat towards the fleet as a safe haven when threatened, but largely operate independently to harass the enemy or engage enemy raiders. Examples: Avenger, Eluder, Fury, Mauler, Nemesis, Probe, Scout, Skiff, Torch, X-Form
Thus, if the player is controlling a capital ship, they can expect most of the fleet to follow them. If they're a cruiser and break off from the fleet, then if there are any capital ships they can expect most of the fleet to stick with the capital ships, although they may draw a couple of supporting escorts with them. An escort or raider that splits off is likely on its own, although they may be joined by a wingman with similar movement characteristics.
As an added player, the player might be able to change the designation of individual ships on the fly, possibly including a 'flagship' designation (which becomes an even higher priority than capital ships).