[X][FLEET] Many Fleets. Smaller fleets will struggle to address determined resistance and force you to bring in reinforcements from other fleets, but can be produced in greater numbers, allowing you to more reliably cover ground.
[X][DOCTRINE] Retain Territory Defense Doctrine. Ultimately, Virmire remains a world with its back against the wall, and any offensives you make must be made only once you are sure of your position. Turtle up, and turtle harder. Make your space a brick wall, against which the Rachni might break themselves. You will serve the larger struggle with the forces the Rachni must devote to bottling you up. Will not cost additional resources to implement.
[X][MARINES] Grant Tannuvael's request. Now that the fight is moving beyond your space, there is a need for an elite, navy-integrated ground force responsible for void-borne operations. Will require an eventual fleet-wide refit.
So, I've found this quest, and it was an interesting read.
As of current question...
Ultimately, our colony is small. 5*10^9 with, I would guess, no more than hundred million born every year. Even if we clad all of them with flashlights and cardboard, we would be unable to sustain groundside fighting without orbital domination. Therefore, I wouldn't go for Ground Forces focus.
Raiding focus is looking good, but remember, we had denied Rachni entry into Sentry Omega cluster while having vastly less resources than them. What is to stop them from using this experience and make any attempt to insert raiding force too expensive for us?
As numerous posters noted, Fleet Battle is not exactly suitable for us. Decisive battles generally favor those in possession of bigger & better forces first and defenders second, and we don't have forces to spare. So, we have to build up, meaning we end at Territory Defense Doctrine in any case.
As for Marine Corps... Establishing entire new branch means Navy would have to get new armsmen somewhere, and we get lots of ground-fighting forces. Considering that we have Navy as our top priority, I wouldn't go as far and just grant the request.
Anyway, if we had established Marine Corps, there would be question of the army and what to do with it. IMO, better to avoid the question altogether, and if we would need regiments of men in droppods - we can establish them within the Army.
As for Big Fleets vs Many Fleets... IMO, Many Fleets is a better choice because a smaller fleet is easier to handle, and considering that we don't build dreadnoughts and are at massive disadvantage in terms of production, we have to have a flexible and mobile Navy.
Multi-fleet engagement should be handled by the top brass in any case.
P.S.
Some questions.
Collision with a sufficiently large asteroid at sufficient velocity can shatter the Relay, as shown in ME2 DLC Arrival. So, can we reposition some sufficiently big asteroid (I'm talking at least dozens of kilometers big. Better if it would be hundreds) sufficiently close to Sentry Omega relay in Attican Beta system, riddle it with tunnels, bases and mobile anti-ship missile (Read 'rebuilt torpedo') batteries and rig it to blow to deny Rachni usage of Attican Beta system / Atiican Beta-Sentry Omega relay?
Can we move asteroids to other relays and blow them in such a way that their (moving) debris would deny Rachni safe navigation into Attican Beta cluster for some time?
And, (hopefully) not a stupid idea this time - does our command have any statistics as to what was effective and what was not? Could we order some sort of study for Learning/War action to open further research (Like, "Bigger guns have shown their effects. Our ships fundamentally use not quite effective older ones, but we have such and such projects, and only if we got, say, some fifty thousands of credits..." or "Torpedoes are hardly countered by Rachni ships. Can you assign some funding to development of new torpedoes and their delivery systems?" or "While reclaiming of Attican Beta was a epochal victory, communication logs show potential pitfalls with the rapid development of our Navy, as current communication protocols are not quite fit to battles including hundreds of ships including capital ones, and...")?
