Plan: Magellan but am worried about what happens if an enemy gets in close.
Short answer, that is what the Plasma Cannons are for.
Long answer, as a a grand cruiser there are two types of enemy we will face, Lesser (heavy cruisers and below) and Peer (grand cruisers and battleships), that will each have two preferred engagements (Closing or Distanced). Which gives us 4 very broad types of engagements. I will start with the lesser encounters since that is what the Magellan is built to primarily deal with.
-Lesser, closing - Any ship built for a closing encounter will have better engines than us at this weight bracket, given the 3D nature of space encounters this makes it all but impossible to prevent them from getting close
if they want to. With a primarily long ranged arsenals we can start to damage them as soon as they enter range, given the volume of fire we can destroy or ward off large quantities of these ships. If they do make it to medium range the plasma goes to work, strips their shields, and then we either alpha strike with the lances or teleport a boarding party.
-Lesser, Distanced - These enemies want to engage at long range, which is fine for us. We almost every weapon we have can reach them to answer the duel. Of the three long distance weapons (Torpedos, Lances, and Small Craft) or compliment of PD weapons makes us heavily resilient to two of them. Given the increased HP, armor, and shields of a grand cruiser we are likely to win any battle of attrition here even against a large force.
-Peer, closing - a peer ship will likely be as fast as us or maybe have .5 Gs acceleration over ours. This means we do stand a great chance of controlling the range and keeping away from them. The strategy is boils down to kite them and shoot. This would take awhile and only works if we don't have a strategic object to protect. If one of these gets into range we are going to get seriously hurt, but with the plasma we can churn through their shields and then teleport over boarders. Likely can win a 1:1 with a some wounds, more then one is run away.
-Peer, distanced - a peer ship designed for long ranged combat is probably our worst match up since they will have more long ranged hvy weapons than us. Our point defense will hamper some of their attacks, but this would be a rough fight. We might win a straight 1:1 with heavy injuries, but it would be dicey. Our hidden ace is once again the teleporters, which have a long range allowing us to board the enemy from extreme distance.
Some closing thoughts. As a grand cruiser we will not have the luxury of controlling the distance in most of our fights, so we need to be prepared for enemies that don't want to get close to us. As a fleet flagship we need to be prepared to fill a variety of support roles and serve as a back stop of the fleet. Long range weapons give the largest zone of control creating a threat in being, something the enemy has to respect even before the battle starts. This can be used to shape and control enemy fleet deployments and movements before the first shot is even fired.
Edit:
@DecaffeinatedOwl , I love it!
@Derpmind, stay strong this will likely be the most complicated ship we ever design