Large reparations for peace isn't a flaw. Other games have different mechanisms, but usually suing for peace is depicted as an expensive proposition. Two reasons: 1. that is accurate; and 2. it prevents the player from manipulating the AI through quickie wars. Not at all a bug.
I'd say warfare is broken in the sense that the tech leveling system is broken. If you wait too long to go to war, it seems your enemies have better ships than you, but the only way to ramp up your gear is through leveling which has the theme of "do something in an area many times to get better options in that area". A passive tech investment system would be better. E.g. allowed to build one research building per colony to generate research points.
This is obviously a keep-it-simple-for-the-kids design issue.
AI invasions do come too often. It would be good if there was a way to interdict a fleet enroute to your planets, and a way to count ships so you know when it's safe to leave your planets. But usually the best defense is a strong offense, so if you are at war it's best to just obliterate their planets until you sue for peace. It would be nice if there was less micro-management in rebuilding defenses, and if the "uber-turret" was available much sooner.
The abduction ray is pretty slow. I always go in low when I use it. I think they did that so your ship would be vulnerable when abducting under some circumstances. The ray should work faster when you are at lower altitude.
Twining species is more a problem with the Sporepedia. It doesn't look at species as names, but as graphs. In my games I keep running into several creatures named TREE, Tree, and Tree, all having different eating habbits and forms. Same if you save minor changes to a creature, the program thinks they are completely new.
A default option for setting building types on planets would be nice.
Radar tracking the enemy as opposed to the cash, would be nice. I'd like to toggle it from: cash/mission target, enemy, food web.
Until I realized they cloned the Civ4 city scroll buttons in the city view, I hated rebuilding my home planet after an alien attack. I was flying from city to city.
My flaw list:
Combat is fun, but I wish there were more techs, more weapon types and countermeasures. It's basically just close attack: laser/pulse, or ranged attack: missile/bomb.
Anti-UFO defense pretty much just come in one flavor: weak-*ss, excepting the uber-turret and if you squat at low altitude over an enemy city. Cities need a turret-govenor to allow automated rebuilding. Turrets are way overpriced compared to on the homeworld.
No way to interdict space travel. E.g. no space piracy against trade routes, no attacking ships before they reach your planet.
Doesn't seem to be any kind of material build-up of enemy forces, just timed spawning. Would be preferable if the enemy built up forces, maneuvered, etc..
Not even the sun is spotless. And though the space phase of Spore might be one of the most innovative space games ever, there are many flaws, some of them even making the game unplayable.
Here are some:
* War diplomacy is broken. A human player can only make peace by playing an enormous tribute.
* Warfare is broken altogether. Seizures of planets are too fast. AI invasions come too often. AI does not seem to have the ability to retreat.
* The radar points out artifacts or money bags even during battle. This is annoying. Point out the closest enemy, or turn off.
* The player might meet a "twin" race, with identical name and appearance.
* Forced building editor, whenever a new colony is founded.
* The abduction ray is too slow and clumsy. Might add to game atmosphere during early game, but gets annoying over time. Should be able to upgrade.
Have you found any other flaws that ruin the experience of space?