I don't see how spamming colony ships is nessacarly a bad thing. So long as you keep a balanced budget, and don't burn yourself out in the process, there shouldn't be any problems. In fact, I would go so far as to say that one might ruin their chances at winning at this game if they don't do a good job at colonizing planets.
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I have another suggestion - introduce planetary invasion MUCH earlier in the gameplay.
I think this is a bad idea. Invading a planet might fail, but colonizing a planet always work. Also, to invade a planet, you have to be at war which slows down the rate you aquire planets, largely because your industry is being geared to war instead of colonization. Plus, any race that avoids war is left free to colonize the planets the waring nations are missing.
I don't know about you, but I'll stick to colonization.
Maybe cut the range of early ships in half and colony and troop ships in half again - let range be slowly researched and developed?
That wouldn't work well. Get a level or two in life support tech, and maybe install a life support module or two, and you should be able to travel maybe 2 to 3 sectors away from a planet. Use starbases, and you can extend the range much further.
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That said, right now I can only think of 3 things that would give me pause, or make me stop colonizing planets altogether.
1. Economics
Somehow I run out of money, and thus I'm unable to fund my factories to make more colony ships.
2. Nerfing
Somehow, I'm prevented from colonizing any additional planets. It has nothing to with player skill. I'm just prevented from doing any further colonization in either an unfair way, or in some unusual manner.
3. Tactical Decision
I decided that it would be more prudent of me stop colonizing planets early so that I might prepare for war.