Actually in stock refitting is a terrible idea. Mostly because it costs 150% of the money to refit and it's usually not worth it unless you use retrofit series. Ripping out a component costs 50% IIRC so ripping out components is generally a bad idea. Keeping a big fleet around to retrofit out is generally a bad idea in stock. If you're building a war fleet, you should be preparing to attack.
Bigger ships in stock are better. Always build the biggest ship you can. Never fall behind on ship hulls.
The main thing in stock is you start with either 20k, 50k or 100k research points. So you open either one theoretical area or two. Theoretical areas are the bottlenecks in research early game in stock.
I like military science for torpedoes and point defense. I like physics for shields. I like construction for fighters, troops and mines. Certain theoretical areas are complete losers in the beginning like astrophysics and industry.
For stock it's best to use "the clone" or the max/minned Empire I showed in the link. There's variations like getting religious trait, but not too many. With that empire you can build a colony ship on one turn with emergency build. Expand, expand, expand. If you see an enemy plop down a colony and build weapons platforms and mines. Try and establish a front line as soon as you can. Build the "outpost", the sole building at the front line that'll serve to mark your territory as soon as you encounter an enemy ship. If the ship is an armed scout, kill it. How? Ram it. All your colonizers should be set to ram. If you see a scout on the far edge of the system, plop down a colony and build a weapons platform. You'll beat it. The colony is now your outpost. Later colonizers should colonize the systems behind.
Satellites are good in the beginning but only on warp points. Fighters are good only on an unprepared enemy. Mines are good early to mid game. Later on, when fleets get into the hundreds or thousands the only way to stop enemy fleets will be fleets of your own. You may be tempted to research larger starbase hulls and fortify a wormhole. Don't. 50 bases on a warp point will stop 200 ships, but you have no offensive capability and offense wins.
The "optimal" ship sizes are the sizes just big enough to access the larger mounts. For example, light carrier can run large mounts and often when someone goes fighters it's an effective strategy to have a hybrid carrier/battleship that can use the large mount and skimp on the hull research. If you're not going fighters, time your contruction and research to coincide so you pump out the optimal ship hulls. Mounts rule in stock. Always use mounts if you can.
Try and avoid stockpiling a huge fleet in peacetime because maintainence kills. Do not build warships until you reach at least destroyer because anything smaller just doesn't have the room. Scouts to harass and explore are okay as are transports to carry satellites or mines to fortify warp points. The fortification should be one system behind your "outpost" system. Colonize, colonize, colonize, first colonzing
away from your home system as fast as possible. For the first ten turns you should have a colonizer coming out every single turn from your homeworld if you built your empire right and set on emergency build. They should head away from your homesystem as far as they can. The juicy worlds they pass by can be filled in by your second wave of colonizers. Around turn 5 your fifth colonizer should colonize a world in your home system and build a space yard, for when your homeworld goes on slow build. Resist the urge to build orbital space yards. Orbital space yards have maintainence and maintainence in stock kills.
Missiles suck. Fighters against a seasoned opponent usually suck, no matter how many you build. Get Depleted Uranium Cannons up to Level Five, then go for Phased Polaron Beams. Armor is better in the beginning, but once you get around shield IV you'll be fine.
Try and husband your forces. In SE:IV, when you attack you go for the throat. Usually, rushes do not work on seasoned opponents. But it depends on who you are playing and whether it's a multiplayer. Usually people ally with the first person they meet, so they share with trade and research alliances. Because if they don't and it's an 8 player game, you lose.
Use small planets for storage facilities and space yards. Use big planets for resource facilities. Use low value planets for intel and research. Use high value planets for mining. Try and match the kind of planet and specialize... a planet with 150 organics should go organic all the way. Small moons are good for building space yards since there's no population penalty in stock.
That's enough to win you a lot of games in stock anyway. Oh and untrained fleets are next to useless. Combat Sensors and ECM are essential technology, because everybody'll put one or two point defense guns on all their designs that basically renders their ships immune from missiles and fighters. So you'll have to rely on direct fire weapons.
Oh and play people
.
You should also be aware that there are certain very gamey tactics like trading colonization technology and population (another reason why people usually ally with the first person they meet), using 100 police troops with no weapons to raise happiness to jubilant, etc., etc., that even if you don't like you'll have to live with or do yourself. Also a lot of people outright trade technology and there's no in game mechanism to stop it.
When you master stock or get sick and tired of trading population and trading colony tech, then come the mods. Most mods fix some of the exploits to a degree, but once you try the dark side at least once at least you'll know what other people are capable of, even if you don't do it yourself.
When you do master stock and you will very quickly, there's a pro league called King of the Hill on the Shrapnel Games forum for competitive, 1v1 play with stock. Their forums are really the best place to look for information. There's a FAQ that goes into a lot more detail than I ever could. A lot of what I do's become intuitive after so many games and I could go on and on for a few pages and still miss some crucial bit of information. And because the game's been out for awhile whoever's left playing it online will be veteran and will know every single trick in the book.
It only takes one mistake to lose.
Brian