If we forget about the XP aspect and coating/decal/skins provided by the different hero ships, here's how I evaluate which one of the hero ship is the best. By comparing them to the normal ship about what exclusive modules and secondary weapons are available. Simply put, the best hero ship is the one who has the most modules and secondary weapon that are not available to ship from the same tier/manufacturer/class.
With the above argument, only 3 of the tiers 2 hero ships have a selection of modules that differ from the available load out of their tier/class counterpart. Those ships are the Old Morningstar, the PCF Morningstar and the Silesia. The three other hero ships can be made by their non exclusive counterpart and thus offer no tactical advantage. Now, the exclusive choice of module can make the ship hard to pilot, but in my opinion, it is that difference that can provide an advantage by surprising opponents with things normally not available in recruit matches. Now, here's each ship and how they differ from the norm, from the less different to the more different.
PCF Morningstar: Heavy Flaks, Plasma Broadside, Heavy Torpedo, Anti-Missile Lasers, Warp Jump.
The PCF Morningstar possess two exclusive loadout making it the less different from the bunch. The Flaks can provide a great surprise against targets such as corvettes and destroyers that get really close and the Heavy Torpedo provide a different type of nuke to the ship that has a faster reload time but shorter range but that can be compensated with a good warp.
Old Morningstar: Heavy Flaks, Scattergun Broadside, Flechettes Missiles, Tractor Beam, Warp Jump.
Similar to the PCF Morningstar, the Old Morningstar can surprise opponents that get really close with his Heavy Flaks and Scattergun Broadside. However with both its secondary weapon and modules having short range require a good use of the warp jump. The tractor beam can offer a great surprise against opponent since the Old Morningstar in recruit that has this module.
PCF Silesia: Machine Gun Turrets, Rapid Fire mode, Drain Missile, Disruptor Pulse, Armor Amp
The best hero ship in my opinion is the PCF Silesia, since it offers a completely different loadout in contrast to the Furia. The Machine Gun Turrets make a great addition to the ship by allowing a constant stream of fires by alternating between the 1st and 2nd weapon reload time. With energy to weapon, the rapid fire mode can destroy nearly any ships except for Navs, is never expected and unlike siege mode, doesn't drain energy nor stops movement. The drain missile combined with the rapid fire mode can make a guaranteed kill or alternatively is great to just harass opponents. The disruptor pulse will surprise any ships, especially dovers, that get to close to the Silesia. And finally the Armor Amp, despite lasting only 2 seconds offer a 95% damage reduction against anything, thus allowing the Silesia to keep its energy against nuke and missile volleys.