Bug: Land units in sea bases don't actually defend the base, they're just treated as cargo. Surely this isn't intended?
I haven't actually done many naval invasions yet, as that would require the AI to build many sea bases. :-s
I set up a situation in the worldbuilder though: a barbarian base with a couple defenders, and me attacking with a unit from land, and with a foil. In both cases the barbarians defended. So I can't repeat your findings.

Can you give some more information as to where you encountered this, or what exactly happened?
And solar power transmitters are acting as fighter/bomber aicrcraft, and obsolete interceptors and penetrators. Intended??!?
Intended at the moment, but I will no doubt revisit the air unit line at some later point.
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I noticed the APC special ability isn't working at the moment. This is fixed for version 7. With that SA, infantry can move as fast on flat terrain as they could on roads in their territory, and faster than ever before in enemy territory.
I may remove that special ability at some later point though.
Removing roads severely limits the ability of a defender to resist an invasion, because they no longer have a movement advantage over an attacker; they no longer have the ability to whittle down an invading stack through hit and run, to respond easily to pillager units (and farms take *hundreds* of turns to improve, so pillaging = death) or barbarians, or to move a defensive force to defend the city that the attacker chooses to target - because it takes the defender an equal amount of time to reinforce their own city as it takes for the attacker to get to it.
That is in fact all intended.
Civ4 tried to add some Rock-Paper-Scissors (RPS) to combat, but IMO that failed miserably. Reason is RPS becomes pointless if you can have Rock, Paper AND Scissors all at the same time at the same place. Then you just get stack-of-doom warfare without any tactics, and the one with the biggest army wins. What fun.
Reducing mobility means it's harder to have Rock, Paper and Scissors always present at every spot. So stuff like scouting, preparing ahead, harrassment of weak spots, opportunism, positional warfare can become more important. That's at least the goal I'd like to eventually achieve.
Regarding pillaging. I *want* to make that a bigger part of war strategy. Note that no one is forcing you to build farms and boreholes. They have a higher yield, but they also carry with them more risk: being pillaged. That's their design: high reward, but high risk. So in areas which you are unable to defend well, you can always stick to greenhouses, mines and windmills. Less big of a deal if they get pillaged.
How to deal with an invading stack of doom?
You can always try to slow down the invaders, giving you more time to reinforce.
Build Perimeter Defenses for instance, forcing the invader to spend some turns reducing base defenses, unless he wants to lose lots of units taking the base right away.
Or build some static defenses, ie bunkers. Not a good idea for your enemy to leave those around, unless they like being bombarded constantly. Destroying those takes time and health.
I also hope to eventually add a limited number of special ability 'spells'. Stasis Generator for instance could immobilze a stack or some units for some time, again buying you extra time.
Also note that in unmodded Civ4, 33% of a city's buildings are destroyed upon conquest. In Planetfall this is reduced to 5%. I might even make it 0%. I also plan to disable razing cities.
This means that in unmodded Civ4, losing a city is a disaster, lots of buildings permanently lost. In Planetfall however, losing a base doesn't have to a big deal, if it is only temporarily. You can get it back in pretty much the exact shape you left it.
So an invading stack of doom doesn't have to mean disaster. Instead of trying to counter the stack of doom directly, you could send some harrassment/pillaging forces in HIS territory, while his forces are concentrated elsewhere. Or you could let the invading stack capture the target base, and then wait him out. If he moves his stack of doom to a second base, the first base captured is less defended, so you can run around his back and recapture it. If he splits his stack in two, so that he can keep protecting his first captured base, well, two smaller stacks are easier to defeat for you than one big one.
If I can add a limited spell system (ie remove all the for me useless stuff of the FfH spell system), I also plan to re-add supply crawlers. I would give them spells which allow them to create units for a gold cost (justification: they're built with nanites). So you'd have mobile production centers which you can move closer to where the actual combat is happening.
It is also making the AI players totally unable to cope with barbarian planet units pillaging; they can't kill them fast enough because they can't get to them, so all their improvements get pillaged, and their economies crash. In a mod where the yields from former improvements are so high, this is a big problem. Particularly so when the AI doesn't understand how Planet works, and so will get lots of native life uprisings.
I'll watch out for this.