Yeah I also miss the old +3 adjacency Capital. I have a suggestion, that solves all problems: Make the Capital upgradable. It could start as it is now. Later in the 2nd and 3rd era, you get the option to research the technology to upgrade the Capital. This could increase the max population on the planet and also increase the adjacency boni.
max pop (increasing in two steps): Cities wouldnt be needed anymore, which would essentially give you a free tile. And it would improve Morale management.
adjacencies: the first tech could improve them to +2, the 2nd to +3. The Capital would become an important factor in the development of the planet again (like it was pre Crusade - and a Capital should be important like that).
Then there could also be a "Capital Specialization Tech" after each upgrade:
a) +1 All Construction per Capital LVL
b ) +1 Research per Capital LVL
c) +1 Income per Capital LVL
This would enable Capitals to work as hubs. I think it might be too strong though, if it works on all planets. So maybe this Specialization should only work on the Capital City, not on the Colony Capitals.
Another idea for a Specialization Tech for Capitals could be: a) +X High Morale; b ) +X High max Pop; c1) X/2 Morale, X/2 Pop ; c2) +1 Terraformed Tile
Since all of these would only be made available throughout the game, the player would really "feel" the development of the capital.
So, what do you guys think?