[quote=Slypheed]
There is no one particular part that is stumping me, its the whole thing o 3oI get that there will be a standard set of upgrades for all, but don't really get the rest. o.o
[/quote]

Okay, let me see if I can explain it better. 

Fighter aircraft (which includes attackers, multirole, etc) are split broadly into [url=http://en.wikipedia.org/wiki/Jet_fighter_generations]'Generations'.[/url] What defines a 'Generation' of aircraft are the sophistication of its' onboard systems and the materials used in its' construction. 

Most current aircraft are Fourth Generation, with modifications and new versions making them 4.5th Generation. Aircraft currently coming into service, such the T-50, F-22 and other are Fifth Generation aircraft. Some on the drawing board (or at the 'back of napkin' stage) could be considered Sixth-Generation. 

In this setting, many of the UN's Fifth and 4.5 gen aircraft have been destroyed or greatly reduced in number, leaving a large number of Third and early Fourth generation aircraft around the world, hence the reason for the list of available aircraft in the OP not including many 'modern' aircraft. 
To keep these aircraft competitive with those used by the UNWO, Avalon has begun a crash-program of refitting them with systems used by 4.5th and 5th gen aircraft. 

These include, but are not limited to, newer, more powerful engines (potentially with [url=http://en.wikipedia.org/wiki/Thrust_vectoring]thrust-vectoring[/url]), rebuilding with advanced materials (such as carbon composites, greater use of lightweight alloys), reprofiling edges (like on the F-35, F/A-18F, etc) for increased stealthy characteristics, increased automation and replacing of avionic systems with modern components to save weight and increase processing speed, power and functionality and using [url=http://en.wikipedia.org/wiki/Helmet-mounted_display]helmet-mounted sights[/url]. Changing cockpit systems from dials and analog 'tape' style readouts to focus on a more [URL=http://en.wikipedia.org/wiki/Glass_cockpit]Glass Cockpit[/URL] layout with multi-function touch-screen displays and adding new systems like modern [url=http://en.wikipedia.org/wiki/AESA]AESA radars[/url], targeting and navigation systems (like [url=http://en.wikipedia.org/wiki/Targeting_pods]laser/IR targeting pods[/url] such as SNIPER and LITENING) would also be possible and likely. 
Adding an in-flight refuelling capability would also be common, as would adding the capability to take-off and land from an aircraft carrier. Things like additional [url=http://en.wikipedia.org/wiki/Conformal_fuel_tank]conformal fuel tanks (CFTs)[/url] could also be added. 

Additionally, the upgrading of these aircraft could also lead to expanding their range of weaponry, adding modern weapons such as laser or GPS-guided bombs, advanced models of air-to-air missiles and a wider range of air-to-ground missiles or other ordnance. 

What you choose to add to your aircraft is up to you - it depends on what you think would be useful, and anything you thinkl that would give your aircraft an edge in the field, and make it cool and fun to pilot. 
There will be opportunities to upgrade your aircraft later if wanted, but at the beginning, your aircraft will be modified to deal with more advanced enemies as they come, rather than being cutting edge.