This topic has been debated several times before, but with no decisive outcome.
As it stands now, Plymouth will destroy Eden in no mark games, and Eden will destroy Plymouth in 200+ mark games.
As I see it, balacing this will be a hard nut to crack. If Eden is strenghtened much, Plymouth loses it's early advantage, and will end up as "the far" weaker of the two colonies. However, because of this shifted balance early in the game Eden players -usually- don't survive long enough to make use of their later advantages.
So, one can not simply chose to strenghten Eden without looking at the repercussions this will have on Plymouth.
So, here's a few of my own suggestions(some of these might need to be mixed and tweaked a bit):
1) Take away Sticky Foam's building damage. (This will present Eden with a possibility for a Static defense)
2) Upgrade Eden's Guard Posts initial Armor. (Might shift balance later on if game breaks down to amount of defense you can have. In addition Plymouth already has a clear disadvantage when it comes to late game offense)
3) Let a new research upgrade Lasers firing range by 1 square. (Combined with suggestion 1, Eden can now take out enemy Sticky Foams
4) Let Eden lynxes start out with heavy armor. OR Make Lynx Armor upgrade availibly early. (Micro's will be the stronger in firepower, but Eden now compensates for this with tougher Lynxes earlier on)
5) Give Eden a new early weapon. (This will probably be hard to do, if not impossible)
Now in compensation for this Plymouth would need to be strenghtened later on.
For this I'd suggest:
1) Upgrading an existing weapon. eg, ESG mines have longer duration OR slightly upgraded damage in addition to damaging structures aswell
2) Adding in a new research for Either: Upgraded Guard Post Armor OR Upgraded vehicle armor. (This would be a late research, after tigers are finished etc)
3) Implementing a new late weapon. (Again tough to do)
4) Make ESG Missile availible. (This is an idea toyed with by me and a friend a long time ago. This would be better if ESG mines had a longer duration.
NOTE: ESG Missiles would leave ESG mines in same field size as the EMP Missile)
Just remember that we can not simply upgrade Eden in early game without giving Plymouth a new feat for long mark games.