If they are not getting bonuses from the scenario itself, then keep in mind that different races have different tech trees, which gives them access to variant techs than what you have with the race that you are playing as.
1. Population is directly tied to your raw production value. You want as much of this as possible. More production means you build things faster, get more money, more research, etc. Naturally, the more people you have, the more you can get done, right? Population is capped by the planet's class (how many tiles it has) in v3.0, so you only need enough improvements to get your population cap to this number.
2. You should specialize your planets. This is the basics to maximizing the efficiency of each planet. Outside of a few mandatory buildings, like cities and approval, most of a planet's free tiles should go toward only one type of production. Not every planet needs to have research. Pick a few planets with the best research bonuses, build a couple of factories to boost manufacturing, and then set the majority of the remaining tiles to research buildings. Do the same for financial planets. Manufacturing planets only care about having a bunch of well-placed factories. This leads to the third question....
3. Not every planet needs a shipyard. As mentioned in number 2 about specializing your planets, you only need shipyards on planets specialized in manufacturing. To take it a step further, if you can, find a cluster of 3 or more planets that are within 6-10 (max) tiles of each other, and make all of those planets into manufacturing planets. This cluster only needs 1 shipyard. This way, you can pool all of those planets' resources together to build expensive ships much faster than you can on individual planets.
4. Generally, if you want to base your weapons and defenses on the enemies that you are fighting. If your enemy specializes in missile weapons and beam defenses, then you want to build ships with missile defenses and kinetic or missile weapons. If you have time to research, however, it is best to research all 3 defense types and have all three types on all of your ships. This is because different enemies will specialize in different weapon types most of the time, and it would be a hassle to make a specialize ship for each of your enemies. You can get away with just 1 type of weapon, however, if you are tight for time. You just need to pack on enough of it to deal decent damage. In this game, having a large fleet of glass cannons, defense-less ships with high attack power, will beat well rounded fleets any day. Who cares about defenses when you can just blow them all up before they have a chance to hit you.
5. Early on, I like to focus on capturing planets while rushing to build up get the infrastructure of my home planet, with a focus on research. Spread your Ideology around to make sure you get the Arbitration Center (Pragmatic), Intimidation Center (Malevolent), and Missionary Center (Benevolent) first. After a decent number of planets have been captured, then comes capturing resources. With version 3.0, resources have become extremely important to ensure that you have plenty of else it will bottleneck all of your development further down the line.
6. There is, but it is kind of meh. https://galciv3.gamepedia.com/Official_Galactic_Civilizations_III_Wiki