First all I must say, loving the game! I thought it might be like another Galaxy At War or Clash of Clans, however it is nothing like it!
I have a few suggestions I would like to share:
Alliance Improvements:
1) it would be a great idea if you provided the ability to reinforce other alliance sectors, as well as request a sector reinforcement.
2) Add more alliance features such as power ups, ability to upgrade alliance level (Provide an alliance command that can be upgraded as well as have troop garrisons for rallys and protection from incoming attacks from unfriendly (enemy) alliances, add alliance only exercises, joint alliance operations, territory control (allow alliances and allies to share control of a territory, add garrisons to controlled territory.
3) Add ability to share EXP from alliance missions.
General Improvements:
1) As stated above; Provide ability to add additional construction slots. Perhaps based on VIP level or ability to purchase additional worker (example: Click Engineering, down below add option to add Worker (Builder etc) pay using shards.
2) Allow for outposts to construct additional resource collections, or a single resource at players discretion (or for added fun, ability to select random)
3) Add chat moderators, although chat filter seems pretty tight as it is.
4) Add new resource (Something rare and futuristic in nature).
5) From within Global Network, allow for trading with other players, allow trading of resources, buffs and alien components. I think this would add some great beneficial in-game economy.
Hero Improvements:
1) Add new building maybe called (Hero Command) with the ability to upgrade hero, such as add armour, add weapons etc to increase strength, power, agility (speed) etc.
2) Add hero only missions, from within Missions tab.
3) Finally allow player to actively increase hero attributes on hero level up, e.g. 1 attribute point per level until level 10 then 2 attribute points, allow player to add attribute point to selected attribute, e.g. 1 point to attack to increase attack by 1.5% (example only) and add 1 point to speed (adds additional .5% to speed) of course this would depend on how attributes are currently increased.
If I think of more will continue to add to this post.