If you play as the TEC the best cap balance is 4 Kols, 4 Akkens, 4 Marzas, and 4 Sovas. Don't even bother with Dunovs. all they do is waste prescious fleet space. Also, once you have your fleet built up, get rid of any Krosovs you have. They cost the same as carriers and arent nearly as useful. As far as combat ships go, about 60 Kodiaks, 20 Cobalts, 30 Javelins, and 30 Gardas should do fine. 20 Hoshikos are the optimal number for them. Cielos have rather limited uses, so only build 5-10 of them. The carriers are the key to all strong fleets, so if you want to win build tons of them. The more the merrier. Ive won entire games on nothing but carriers, so keep them safe. Also, make sure you have factories near the front. You'll want them to quickly replace any losses you recieve. of course, if its a AI you playing, even on hard, you can destroy their entire fleet and take no damage. Good Hunting and FOR THE HOMEWORLD!!!

1) the best counter to heavy cruisers are bombers.  Other than that, many of the support cruisers are effective at disabling or otherwise thwarting them.  The guardian, hoshiko, subjugator, and subverter in particular are your best bets.

2) Again, bombers.  They deal the most damage to orbital structures.  Other than that, LRF are a good alternative. 

3) Vasari are strong early game, and have the ability to negate enemy shield mitigation, making them especially dangerous for destroying enemy capital ships.  TEC has the strongest economy and the cheapest ships in general, which gives them the opportunity to field the largest fleet.  Advent are late bloomers with exceptionally powerful fleets and by far the most powerful shields, making their capital ships the toughest to destroy (unless you're Vasari...).

4) for Advent, my first three capital ships are almost always the mothership, radiance, and halcyon.  I sometimes swap the order of radiance and halcyon, but mothership is always first.  This is called the "holy trinity" and they are some of the most powerful capital ships in the game.  The other Advent capital ships are good, but not as good. 

For Vasari, the evacuator is a must-have first choice.  After that, anything is possible; all the Vasari capital ships are well balanced and powerful, and picking the right one for you involves evaluating the situation and making a decision.  I personally I like the Vulkoras for bombarding planets, but the Skirantra carrier and Kortul battleship are also two of my favourites. 

As for TEC, you usually want to have an Akkan, Marza, and Kol at some point in your fleet.  Their abilities are extremely useful.  However, Dunovs are excellent for restoring shields and for other support abilities.  It's common to see Dunovs working in pairs, so they can restore each other's shields.  Sova is a little weird, and often times I ignore it altogether, but in some cases its embargo ability is invaluable.

First of all, it's very rare to get 16 capital ships in a game (unless you're playing games with over a hundred planets).  So that's not very useful advice.  Secondly, Dunov is an extremely useful capital ship and should not be ignored.

The best way to deal with that Kodiak spam is bombers, colbots, and hoshikos.  Here is how. 

1. You notice he is teching up military labs.

2. Start building LRFs and tech up carriers and hoshikos.

3.Try to rush him and knock out military labs WITHOUT REVEALING YOUR CARRIERS.

4.Fight any fight according to your normal strategy.

5. Build lots of carriers with bombers for strick craft. Keep them at your homeworld.

6. About this time he should be owning your fleet with his HC fleet.... Retreat.

7.He follows only to jump in on your bombers and they eat away at his fleet.

8.Work on teching up to Demolition Bots for your hoshikos, only build hoshikos, colbots, and carriers.

9. If he retreats, follow him with everything you got but any LRFs you saved.

10.  He is now frantically reseraching guardas, and not making more HCs.

11. The final fight micro manage.

Micro your bombers away from his garda's (cuase any competent spammer would have gardas).  Pray to the DEVs that he follows your bombers with the garda's.  Have the demolition bots ability for hishikos.  Demolition his guarda's.

Watch as your bombers tear apart his expensive fleet as his guardas desperatly try to return to cover them.

Use your Colbots to kill his guardas.  Battle won.  Thoughts?

1. Heavy Cruiser spams are, as others mentioned, easily countered with Bombers or your own Cruisers. With TEC, Hoshikos with Demolition Bots can halt some of them, and massed LRMs is also fairly viable.

2. Not sure about Entrenchment, but in Vanilla Sins, try using Arcovas with Timed Explosives. Just four of them can take out a structure, and they're very cheap. Also, the Marza Dreadnought's Missile Barrage can cripple massed structures, and Bombers have a damage advantage against structures.

3. Generally, TEC has ships with average fleet cost, strong hulls, and good firepower. TEC's main advantage is economically; good Trade Ports and Refineries makes obtaining and fielding forces very easy by mid-game. Vasari has strong, but more expensive ships and rely on mobility. Their phase missiles can bypass shields, which is an enormous benefit against Advent foes. Vasari culture is the weakest, but their resource upgrades improves both Metal and Crystal at the same time. Advent has cheap, but weaker ships that rely on abilities. I'd say they have the best capital ships; all of them can be very useful for a strong fleet. Otherwise, Advent's best points are their defenses and culture; they can set up the overall best fortifications and their culture spreads the fastest.

4. The amount of capital ships, and their combinations, depend entirely on the map and enemy factions. Smaller maps will rarely have more than 3-4 capitals per side, while multi-galaxies can have large combinations.

For TEC, the Marza Dreadnought is always a solid first choice. Good damage, and Missile Barrage is arguably the strongest ability in the game. Akkan Battlecruiser is good for large maps with its Colonization and free extractors. Against Vasari, I highly recommend starting with a Sova Carrier. Early Fighters makes fighting off an Assailant attack considerably easier. Kol Battleships aren't great starting ships unless against Advent and played in pairs. The Dunov Battlecruiser is one of the worst choices as a starter, as Shield Restore isn't as useful early-game, though it is an option with EMP Charge.

TEC combinations are among the more varied. Marza Dreadnought is always good paired with any capital ship, especially with the Dunov Battlecruiser. The Marza auguments Dunov's low firepower, while the Dunov aids in keeping the Marza alive. Kols are strong in pairs, as the two using level 3 Flak Burst will destroy entire SC squadrons quickly. I recommend a Marza Dreadnought with two Sova Carriers. The Sovas can clear out any Bomber threats to the Marza, then quickly establish defenses by a cleared planet with Rapid Manufacturing.

Yet another reason I prefer "highlight and jump".  If your fleet's getting creamed, group jumping might be it's bane.  Highlight jumping will get at leastsome of your fleet out of there.