Side-topic :
1. GTVA ships don't have a very strong hull . And upon some part of their ship's hull getting destroyed , the ship becomes unstable ( air being sucked out by vacuum into space , and it takes time for the airlocks to lock the damaged place IF their ships have airlocks there ) . Second , when the beams attack , not only do they breach the hull , but also heat up the air inside the ships to very high levels , rendering most subsystems unstable ( that explains why ships sometimes still fire when the break ) . And since the ships is shaken by the beam power , the air is extremely hot and the air leaving issue , the warheads explode also . Reactors eventually explode too .
2. Meson bombs are based on sub-atomic particles called Mesons . They are composed of a quark and an antiquark, and have masses generally intermediate between leptons and baryons.
On-topic :
I believe that the Shivans aren't toying with the GTVA , but rather preparing them from the "bigger problem" . They are fighting them to make them improve faster . When the GTA and PVN were at war , they hardly advanced . From what I heard , Orions and Typhoons were their only destroyers during the whole war . Only when the Shivans came they started advancing . And in FS2 era , the shivans returned to get them to improve even faster . Because GTVA's advancing slowed down during the NTF rebelion . Making the Capella star go supernova was also another thing that the Shivans wanted the Terrans and Vasudans learn to stop ( stop stars go supernova BEFORE their time I mean ) .
Anyways , those are just ideas .
By the way , sorry if this was already mentioned , I read only a few parts of the topic 
Side-topic rebuttal:
I believe you underestimate the GTVA's engineering and overestimate the superheating ability of a photon beam cannon. GTVA ships undoubtedly have airlocks standard on most all of their large ships. This Hippocrates is an obvious showcase of this. It says in the tech room description: "
The unusual design of the Hippocrates enables its crew to isolate sections of the ship quickly in the event of quarantine or hull breach." Also, when the Colossus fought Koth and his destroyer, the on-duty commander of the Colossus mentioned that they had evacuated forward decks and were preparing for the impact of the Repulse's suicidal attempt. Also, it's intellectually dishonest to say that a space-faring race that has mastered subspace, nebular mining, built a Juggernaut, and has developed a unique method of communicating with the Shivans simply doesn't think to put in airlocks for critical decks, that is, if they don't already exist in every corridor of the ship.
About the beam cannons:
Go back and look at the FS2 intro. Tell me how long it took for that first-generation Lucifer beam weapon to go through that Orion destroyer...less than a few seconds? Also, if the beam cannon is really heating up the air inside of the ship, how hot do you think that air is once the beam breaks through the hull (in a matter of milliseconds, I might add) and is released into the "Absolute-zero-cold" vacuum of space? If I was a ship designer, I would be a bit LESS worried about the residual heat of a beam cannon's impact and MORE worried about the gaping hole that now exists in my weapons subsystem. It's not like the engineers know how to deal with heat, anyways: fusion reactors, overcharging first generation high-yield juggernaut-class beam cannons? Excuse me, but, holy ****; that's a heck of a resume.
About the Shivans:
It's all about subspace. The Shivans were only aroused when the humans and Vasudans entered subspace. It's weird to see it this way, but the Shivan's probably aren't toying with anyone. Ask the Ancients if the Shivans toyed around with them. I'm really sticking by what Alpha 1 said at the end of FS1: "The Great Preservers". Nobody knows just what kind of effects the use of subspace will cause in the long run; what if the constant use has negative side effects, like the galactic weakening of jump nodes, not just active nodes, but a system-wide shutdown of all subspace travel!? I also believe that's why the Shivans left the Knossos portals intact. The Ancients may have been arrogant, but they weren't stupid,
or they just didn't know what they had. By keeping the Knossos portals alive, subspace travel between systems was preserved.
Here's a thought. What if the detonation of Capella not only created a new portal, but has a universal effect on subspace itself? The rippling energy emanated from Capella before it's destruction could only be a precursor to some fantastic going-ons after the supernova of the star itself. We won't know because everything in that system just got annihilated; but I'm sure the Shivans are more interested in keeping the fabric of space intact than military conquest. It's been noted many places that if the Shivans really were planning the systematic destruction of the GTVA, it would have been much easier to send one or two Sathanas juggernauts to each system, instead of consolidating them all around each individual star and causing a cataclysmic explosion. Well, if it's not destruction, the only other motive the Shivans had for doing anything was...preservation...
