First of all you should put the feeding system of the heavy bolter for the heavy marine, or put the high capacity magazine.
Originally the Exterminatus (EX) heavy bolter (HB) was intended to be a belt fed model. However animating the droop and swing of the belt in sync with that of the carrying marine was beyond our capabilities, so a box magazine was made as a later addition (you may notice the colour does not quite match.) with the move to the orange box engine we now have the option of using physically simulated joints to animate the belt. However since we now have working box magazine changing back to a belt feed seems like an academic exercise.
How can we make the current magazine look more "high capacity"?
In the veteran marine you should put the sword more to the center and the gun all to to right so it looks like more realistic.
In order for the perspective on the melta beam to appear correctly the pistol muzzle needs to be near the center. The pistol used to be further right during the idle and brought to center during firing, however when you started firing the beam appeared to stretch elastically as the pistol was shifted to it's firing position. Which looked bad. So I settled on iding with the pistol more central. As Typh said the pistol is also the primary weapon in the combo, since it has greater range.
Make the chimeras bigger and the thunderhawk bigger, but the harpy smaller and put three in the air not one.
Vehicle scale is a bot hard to judge in 40k, I think we're pretty close to correct scale as compared to the miniatures, but not necessarily realistic (obviously no way you would 30 marines a model Thunderhawk or 10 guardsmen in a chimera model). The EX look has always been aimed closer to the miniatures. If you are going to suggest scale changes a percentage would help us visualize the change.
It would be cool to put a Scout marine with a Snioer riffle and a silenced boltpistol as a playable unit for a special mission or something like that. Also make a unit like the scout but for the tyranids such as a Ravener.
Scouts with sniper rifles have been pretty much ruled out for gameplay reasons. Both the Lictos cloak ability and the high accuracy, high power ranged attack of the Zoanthrope have proved to be very potent in EX beta tests, combining them both would create some kind of overpowered uber class. If we get scouts they will probably end up being a cheap, fast, close range class, with bolt pistols, shotguns and maybe a chainsword (as a counter to an equally cheap genestealer class).
The big thing with Raveners is burrowing, how the hell do you make that work in an FPS?
Make the special weapon operator a plasma rifle it will be really cool.
I would like to have an alternative set of plasma weapons for the Veteran, Specialist and Heavy marine (ie replace melta weapons with their plasma equivalent). It's one of the shortlisted ideas for the 1.1 version (after the 1st public release).