Been a while since I played MoO, so there may be better solutions, but anyway...
Apart from heavy Lasers and Ion Cannons, another thing to counter the Repulor Beam is to equip ships with High Energy Focus (Propulsion Tech), which increases laser ranger by 3. Also, The Repulsor Beam is a double edged sword IIRC; doesn't it mean the ship equipped with the Repuslor Beam can't use short range lasers?

Generally I found smaller ships more useful in the late game, since you could then equip them with so much stuff (defensive equipment and bombs) that they can reach and destroy enemy planet defenses on the tactical combat screen.
In the early game one Huge ship can often make the difference, since it will usually survive to fight another day.
But for some races, with bonuses to ship combat, like the Mrrrshan and especially the Alkari, benefit more from small ships. Small Alkari fighters can be extremely annoying.

The effectiveness of Planetary Bombardment is heavily dependent on the defenders Planetary Defenses. The higher the Shield rating, the better bombs you need to even get through the defenses to do damage.
Personally I favoured a mix of heavily armoured battleships, and extremely mobile fighters for this job, but when the enmy has strong shield it's vital to have as strong bombs as possible. If you can develop fighters that can carry at least one strong enough bomb, but also be mobile enough to dodge most of the enemy fire, then much of the work is done.

You had bad luck with the weapons tech since there are several other beam weapons with 'heavy' versions and some that are inherently longer range. Additionally, various tech (and some tactical tricks) can be used to counter repulsors, although if you don't have any of those then missile ships can do the job.

Hey.

So, if the computer breaks out repulser beams early on, it can be very difficult to wage an offensive war. You can hope to acquire a 2-range weapon -- hopefully something better than laser -- or try and steal one from your opponent if you haven't been able to research one. You can also build huge stacks of missile ships, but you'll need to have enough ships with powerful enough missiles to destroy your targets before you run out of ammo. Torpedoes dont' need ammo, and so would be effective, although the earliest torpedo is anti-matter at tech level 23, which might not be available as early as you need it. Another way to deal with them is to have a higher speed rating. I'm not sure how much more you need to have, but I've been in battles where my sluggy, repulser-armed dreadnoughts would be shredded by faster ships that would move right up to them, fire, and be repulsed afterward. Inertial stabilizers are a good early way to boost speed, but I'm still not sure precisely how much faster you must be to out-initiative their repulseres; just being equal or one better doesn't appear to be enough.

If I may, I would suggest holding off building a large navy for as long as possible. In the early game ships are just not a very cost-effective way of protecting your colonies, and on higher difficulty levels the computer often fields much larger, more advanced fleets than you anyway, so it can be very hard to fight effectively as you seem to be noticing. I would suggest pouring all of your research into planetary shields (steal the tech if you don't get it, it's worth it!) better deflector shields (because those stack with planetary shields) and the best missile tech you can buy. Then build as many missile bases as you can. You can upgrade missile bases to the latest tech by spending on defense, so they won't become obsolete like ships. Planets take half damage from lasers, and planetary shields give a huge defense bonus anyway, so even a single well-shielded base can fight off 10,000 ships if they don't have good enough bombs or missiles. Frequently the computer will not put bombs on on every ship, so target the bombers first. Long story short, missile bases are just much better than ships at defending until the late game when bombs start doing 50+ damage. They're also cheap to build and maintain. Lastly, if you really need a ship -- say to defend a newly formed colony -- your investment in good missiles will let you build powerful, medium sized missile boats that can be effective at beating up repulser-armed ships, or even invading an enemy colony in a pinch, since missiles do full damage to planets, and so might actually get through their defenses. Stinger missiles are very powerful early game weapons, and their 15 damage can still get through shields in the late game.

As far as the difference in planet bombardment effectiveness, that sounds like you're dealing with planets that have different amounts of shielding. Deflector shield tech is always applied to each colony, but sometimes just because the computer can build planetary shields doesn't mean they will on all of their planets. You might have found a planet that had yet to finish their shields.

Now, if you're trying to make a fleet that can actually conquer, well, you need to know what your opponent can build. Spies are useful for this. As a general rule I don't bother building war fleets until my initial grab of planets are fully operational and my front-line planets have some bases for defense. At that point investigate the capabilities of your prey, and consider whether or not you can build a fleet that will actually be effective. Some good questions to ask yourself:

What's the value of their planetary+deflector shields? If they have Planetary shield V and 3 levels of deflector shields I'm going to need a laser that does 17+ damage, or a missile/bomb that does 9+ to even dent them. If I can't field a ship capable of that I won't be able to take a planet with even one missile base defending it. (Well, you could drop biological weapons on it; they ignore shields completely, but since using them causes everyone in the game to hate you I would not recommend it unless you're prepared to deal with a diplomatic nightmare.

Do they have troublesome specials? If they have ionic pulsars or streaming weapons it will probably not be a good idea to field small ships. If they have repulser beams (ugh) we're gonna need a way around those.

And so on and so on... knowing is much more than half the battle. I really recommend building ships only when you know they will be successful, and build only as many as you need, because ideally you're stil researching new tech while you're at war, and soon you'll have even better toys to play with, and so will the computer. The computer WILL build ships to counter yours if given enough time, so don't expect your large navy to be effective for very long.

Hope that helps. Read this website if you have the time or inclination. It's the best and most accessible guide to the game you'll ever find: http://sirian.warpcore.org/moo1/

Thanks for the help everyone, future games have defiantly gone a lot smoother. Building missle defenses has greatly improved colony survivability than trying to defend with ineffective ships. Last game I had one frontier colony kept getting attacked which is giving colonies behind that one time to build up missile defenses. Only using a smaller fleet than I was using before but I'm still gaining ground with them (though not for much longer it seems)

The High Energy Focus special ability I totally neglected. I will make sure to get that tech as soon as I can in future games.

When you are new to the game and get many weapon tech options at once it can be a bit over whelming and totally I over looked proton torpedoes that don't require ammo. Next time I design a large ship, I will keep those in mind too.

I did have bad luck with tech options but I think part of the problem was also me picking the wrong techs. I suppose that's going to happen if you have too many options, and not enough insight into each.

I'd like to mark this thread as solved but all 3 of you pointed out things which have improved my game. But I can't mark all 3 of you :(

Heh, although it occurs to me I forgot to mention the problem with torpedoes... They only fire every other turn! Still, their high damage makes them versatile. Sometimes you just need a weapon that can hurt planets, no matter how slow it is.

Honestly, I think half the fun of this game is trying to make do with the random tech. The games where I don't get planetary shields early game are harrowing, but satisfying. Same with bombs, or good lasers late game. Not really until impossible do I think you run into situations where bad tech draws make victory unattainable. Hell, even on impossible it's probably doable. (Not for me, though. Not yet)