Redesign of Explore class Ship (Destroyer)

I don't think they would even bother with the Explorer class ships. While the have a ton of nice qualities they were built with an entirely different purpose and too many compromises were made. They might be more likely to with scout size ships or captures Jung and build them into gunboats with shields and jump drives powered with zpm. I'm honestly hoping they will find the two missing defenders as Flying Dutchman still intact and just begging for a jump drive. Even as outdated as they were they were heavily armored and built to slug it out, which is exactly what the Aurora has been doing. Their biggest drawback was speed, this disadvantage is practically negated with the jump drive.

I think that if they are building new ships then the technology of all the alliance comes into play. Takaran/ Darvano/ Tannan(Jung)/ Earth(Old and New).

I think that in an explorer style ship build from scratch with all currently available tech would be badass

The engines would be better quality, but scaled back, similar power, smaller engines. (speed is less important with Jump tech, but very handy to have)
2 Forward launch tubes sized for Falcons. The launch tubes could double as launchers for KKV's and AMKKV's, which can be delivered to the launchers directly from stores below the launch tubes/in front to the fighter alleys.
4 Plasma cannons would have they're own spaces built into the nose of the ship. The extra room gained by reducing the size of the engines & Fuel tanks would allow for 4 & 4 side and 2 rear facing Plasma cannons.
Plasma Turrets would be installed topside and underside and used in place of the limited target radius of the plasma torpedoes.
Quads top and bottom, with different rounds ready to load, (solid/ fragmenting/ incinerator rounds etc)
Point defense lasers top and bottom with overlapping fields of fire for redundancy.
All weapons are housed internally (they are raised hydrolicly or have doors that close in front of them) until deployed, to prevent damage in normal operations.
Power supply - Takaran Fusion reactors as backup/starter power for other power sources. 4 properly shielded ZPED's linked in pairs, 8 mini ZPED's linked to Plasma cannons (2 forward, 5 amid ship, 1 rear)
ZPED driven Jump Drive (2 ZPED's should jump an aurora sized ship 10 LY a jump with no charging.)
Semi-separate Energy banks kept charged for a 10LY emergency jump in case of ZPED failure.
Shields for the love of all that is holy! Takaran ones that allow the falcons to fly outward with them still up.
Triple redundancy for all emitter, shield and jump.
Heat exchangers need to be better protected, possibly heat is gathered and disposed of by venting into the propulsion/weapon systems?

I would think that it would be easier to build ships around function rather then adjusting ships to fit that role.
Building a ship around 2 plasma cannons and a ZPED Jump drive would leave you with a ship twice the size of the Scout ships and build a nice little attack fleet. the perpuse of these ships? to 1on1 gunboats and frigates and swarm the bigger enemy ships. I would call them the Avenger Class, because they would be the first ships build exclusively to tackle the Jung since they attacked earth.
Que Fabricators!!!

I'm not say the alliance won't build purpose built ships in the future, which incorporate all the the technologies of the alliance, however first they must have full backing for the alliance members, I can image the Ta'keran noble government being very against share ship designs and even more of their tech with the alliance navy. Tug won't have access or permission to share it all.

And any warships capture or found would easier to upgrade to a point.

However to start from scratch requires a lot of design and testing. To begin with the frame of the ship any new framework needs to be designed mathematically, in scale eat... Much easy to take a design already been tested and upgrade it.

Also at the moment the aurora is pretty much the most child for the hopes of the alliance. A another ship Turing up which doesn't look like the aurora won't give the same impression with the right propaganda.

Another consideration is hiding your numbers if you have your ships looking as alike as possible, it's hard for the Jung to tell how many you have. Which could be important in the beginning if they believe the alliance had more than 5 ships as they currently do they will hold off their attacks giving the earth more time.

If the alliance capture Jung ship I don't think they should copy the design, study it used for some cloak and dagger work, but to to have many Jung ships might raise concerns with the the population of the worlds you are trying to save.

In the short term, build frigate size ships; that instead of building a ship and then designing weapons for it, build a huge plasma torpedo launcher and build a box of a ship around it with laser point defense and plasma cannons. Long term, build a battleship size ship with two huge plasma torpedo launchers, rail launch KKV/jump nuke launchers, massive plasma cannons, and a bunch of smaller plasma cannons. Each new ship, of course, would have interchangeable weapons for quick repair.

Examples: http://www.thingiverse.com/thing:760744
http://www.thingiverse.com/thing:761603

Wonder if the alliance will make dedicated carriers and Capitolships ?

Could they absorb the heat from the heat sinks and use it for something like hearing things and the compartments or vent it in another direction away from the enemy ?

A possible new heat sink tech in the data arch? Or possibly layered armor tech that is not sealed and presurised over the heat exchangers... you know for reasons.

I reckon the data arch might provide better H heat reducing technologies, but i don't think they will be able to be incorporated into the Auroras Design with out major rebuild. same with arm. Might be interesting if some some of heat store or converter was found in the arch basically reworking the heat in to power back into the ship. or storing it but having to be released in one big burst of radiation.

I think Ryk has it right with building the scout ships first. Clearing the fog of war and getting some intelligence on the enemy is a major advantage, and on the political side they will also be able to start establishing a presence in the liberated regions sooner.

I would next start building some kind of cheap, scout sized torpedo boat armed with a mini kkv launcher. They would be used somewhat like a submarine in tactics. Find a target, jump in to about 10 light seconds out, take 5 seconds to acquire and launch the kkv, the KKV with an acceleration and travel time of around 5 seconds would hit before the torpedo boat appears to the target. This would be a safe and stealthy stand-off weapon.

All this depends on how small you can get the torpedoes. If you took a Takaran com-drone, stripped it of it's communications equipment, most of it's fuel, replaced it's power generator with a one use battery pack (charged by the torpedo boat), and any other unnecessary equipment removed then I would expect a 'bus sized' drone could be shrunk down a fair bit. It wouldn't even need to go as fast as a com-drone, as at light speeds it would be less about the amount of damage it could do and more about how fast it can get to the target before the target has made course changes.

Jump Scoutships are a good starting point yes, but lets not forget that we have had three waves of Jump ships before them.

1) Jump tactical shuttle
2) Jump Falcons
3) Jump Boxcars
4) Jump Gunboat (Scoutship) (also retooled KKVs hanging from the undersides of standard Gunboats is fine by me, you would just be wasting resources building a KKV launcher when you can just release a drone from the hull of a ship - that can then engage in plasma torpedo strikes of opportunity with its sister ships)
5) Jump Frigate/Destroyers (built around dual plasma torpedo cannons)
6) Jump Cruisers (Aurora / Celestia) (with modified forward sections / reduced fuel storage for six forward plasma torpedo cannons) (Also they were built as carriers, because carriers are far more dangerous then standard destroyers or curisers, give each a complement of Falcons and get them out there)
I imagine the bigger ships will just be refits. Why build bigger the the Aurora when two of her can take out a battle platform.