Given that there were there larger, more organised civilisations in South America compared to NA, why did they not colonise North America themselves?

'Why didn't X happen?' questions are inherently speculative, so in that spirit, here's my wild, uninformed speculations...

Logistics

For Central American states, invading North America would mean moving armies through relatively arid and/or mountainous regions in what is now the Southwestern US. These areas were largely inhabited by hunter-gatherers, and it would have been impossible for an army of any size to live off the land (no crops to pillage). The Mesoamericans didn't have access to pack animals, so it would have been difficult to carry enough supplies to reach farming regions further north. The South American cultures did have pack animals, but they would have had to cross the Darien Gap, which is difficult to do even today. Neither cultures were seafarers, so they couldn't move forces in that way either.

Technology

You're right that the major cultures of Central and South America were more organised, in that they had cities, monumental stone buildings etc. But I'm not sure they necessarily had a significant military advantage over the North Americans. For example, they didn't have metal weapons, or cavalry. They could presumably have organised larger armies than many North American groups, but then they couldn't necessarily support them on long-distance expeditions of conquest (see 'Logistics' above!)

Ultimately, I'd argue that conquering North America is just fundamentally difficult... after all, it took the Europeans several hundred years, even with the help of firearms and smallpox!

It wasn't worth the effort

This comes close to the question why the Roman Empire didn't take over Ireland or Germany: there was nothing there that warranted the effort; the costs would be prohibitive. Admitted, the Romans did try to integrate parts of Germany, but failed.

This applies even more for American civilizations because they lacked three vital necessary components:

• No wheel

That means everything you need to get there or from there to bring home would have to be carried by men or animals. Which they also lacked:

• No pack animals

The Incas had llamas, but the Mesoamericans didn't even have that. That means everything had to be man carried. No matter how you try justify it, that is really expensive.

• No seaworthy ships

Having boats is one thing, seaworthy ships useful for carrying loads economically is quite another. The Mayas had boats, but nothing remotely close to viking longships or Roman ships.

Physical boundaries

Meso-Americans were restricted by deserts. First they had to cross the deserts in the north of Mexico, then cross the same deserts north of the Rio Grande to reach the Puebloans. They probably knew Puebloans existed, but it's doubtful if Meso-Americans knew civilizations beyond that. The Puebloans were far less developed than Meso-Americans, and lived in oases in canyons. I'm not sure if they would be seen as worthwhile for conquest or settlement.

And they would face the exact same limitations: no grains (they had corn, but but not wheat), no large animals, no metals, no wheel, no ships.

Further south the Inca empire had another barrier: the Darien Gap. That's one of the most rugged places on the planet. Steep mountains, vast jungles, dangerous animals and ferocious local tribes. Even today, with our modern technology there is no Pan-American Highway: it stops before the Darien Gap, and continues afterwards. But nothing in between. It still is too dangerous.

In the unlikely event Incas would send expeditions across the Darien Gap, they would be meeting the Meso-Americans. No idea how that would work out. I don't think that meeting would be a happy one for both parties. Perhaps for one party: 'Great, fresh sacrifices walking in.' or 'Looks neat here. We found what we need.' But not for both.

In both cases (Meso-Americans and South Americans) they had no need to expand due to population pressure. The Mayas did have a population problem but never solved it.