Right now Resistance just isn't very useful, it essentially makes invasions of planets a small percentage more difficult. However, it could actually be a pretty useful ability if implemented correctly...

How:
What if Resistance added a long term unrest penalty to conquered planets representing the population fighting back against their conquerors. A planet with a higher resistance results in things like slower production, research, and commerce, construction delays due to tampering, building being shut down due to sabotage, buildings being destroyed entirely due to attacks, ship production delayed due to interrupted shipments, and perhaps even shipyards being damaged if multiple planets are resisting together. Resistance could also allow for an easier counter-attack from the native species. Lastly, if entire sectors are in resistance then they could spawn ships and act as pirates launching guerrilla style attacks on transports and cargo ships.

You can even tie this in with future DLCs and give espionage bonuses to planets being conquered by non-native races because the population is aiding their main race. It'd be easier to get the planet's statistics, military count, info on defending ships, and visibility.

Once we have the "heroes" implemented you could send a character to a conquered planet (chance of being captured going in and during his stay) to help aid in their resistance improving their effectiveness.

Balance:
This would help aid the game's balance as warmongering right now is too easy and without long-term consequence. There should be a penalty associated with invading planets as right now it's invade-and-forget; there is no penalties at all other then a small economic cost of invading and a slight moral penalty if you're too large.

Would be conquerors would have to focus on improving the planet's moral until the resistance dies down or to send in more troops to help quell the uprising. Secondly, the effectiveness of the resistance would be dependent on the planet's native population size so eliminating more of the natives reduces the odds of a successful resistance movement. It would benefit the conquering race to move their own colonists there to act as a buffer to the resistance and creates more loyal subjects.

Population Matters:
With this you could also make it so a planet's population matters. Make a race's population add that racial bonuses to a planet. For example, a 100% Terran planet would give 100% of the Terran bonuses while a planet with 50% Terrans and 50% Altarian would give bonuses of both races.

You could also have this come into a greater effect with tourism and trade simulating migrants moving from planet to planet. Over time your planets would start to have small alien populations inhabiting them giving you some new bonuses but also inhibiting your old and original racial bonuses. The player is then asked to make some difficult choices through events and policies regarding other races.

"A large and damaged ship carrying 1 billion Iconians landed on Mars seeking refuge from the peril within the galaxy. Starving and without fuel you are asked to make a choice as to their fate..."

• Benevolent: Allow them to stay (gain relations with Iconians, +1 billion alien population)
• Pragmatic: Require them to work (+10% productivity, +1 billion alien population)
• Manevolent: Arrest and execute them (+10% moral, lose relations with Iconians)

With this your population suddenly matters and results in interesting choices.

Conclusion:
A lot can be done with Resistance (and population) to make it more meaningful. This all adds to more player choice without too much complexity (MOO2 and StarDrive both already touch on this). Most of all it makes your race important to everyone by making the planetary benefits tied to % of population.