Most differences are clear in the EV Nova Bible.

The most important are:
NCBs instead of Mission Bits - functionality is much greater and they can be triggered in many places, not just missions
16 bit instead of 8 bit graphics
RLEs rather than PICTs as the basic type of Sprite — PICTS will still work, but they won't overwrite Nova RLEs
Different sizes for most of the graphics
New resources - Chars, Chrons, Intfs, Ranks, Shans
Shans introduce a number of modifiers to the way ships are displayed

Careful rereading of the Nova Bible is key.

However, the following undocumented differences have been gathered from board members, and may prove useful.

#1 Speed figures for ships have a different effect in Nova from Override
A good starting point is to double your Override speeds

#2 If you put EVO style spins with PICTs in in slots already occupied by EVN RLEs, they don't load - you have to make RLEs instead.

#3 Visbit settings have to be changed since where EVO used 1xxx as a negator, EVN uses !xxx,

#4 One way hyper links don't work.
In the old game engines you could creatively exploit the fact that failing to make links in both directions would cause a one way link.
Nova automatically corrects this and records the correction in the log.

#5 A xenophobic gövt dude will never attack the player first if its ship type attacks asteroids and there are asteroids in the system.

So to make it behave normally, you either have to make it a no asteroid system or create a variation of that ship which does not attack asteroids. If you don't, the ships will buzz around eating asteroids and ignoring the player.

#6 Auto-abort missions no longer trigger bits in the on-succeed field.

Use on-accept instead.

This is identical functionality, just a different implementation. However, can be confusing if you are coming from EVO.

#7: In EV and EVO, one needed to define a spob's location in both the syst and spob resource. In EVO, if you failed to correctly define things on the spob and the syst, a spob looking blob would appear on the radar, but wouldn't be able to be landed upon.

#8: Looping systems. In EV and EVO, the player would eventually reach a 'wall' in the syst, beyond which they couldn't move. This caused problems when an AI battle would move beyond the barrier, keeping the player from taking part.

#9 Music now requires an MP3 file rather than a res.
This is fairly well known, but is not in the EVN Bible.

#10 Beam weapons tractor beam effect now linked to mass not acceleration

This is noted in the documentation but is worth mentioning here because it makes the gameplay so thoroughly different.

#11 No bounty hunters on domination

EVN does not have built in bounty hunters for dominated planets. You can however create them as an invisible mission which only goes away once the bounty hunters have been destroyed.

#12 Port Authority / EVONE create random garbage in the outfit field of ships
Most of the time the numbers are so high that they are meaningless. However, they may assign something unwanted and unexpected, and therefore need to be checked.

#14 Skill level quite different - make sure you set it for realistic dudes
The skill variable in EVN is based on speed rather than on whatever it was in EVO. By default the variable is 0 in EVN, although both Port Authority and EVONE seem to fill this field with random garbage. However, this results in carried fighters which are released at the same time remaining more or less on top of each other while the player blows them to bits. The problem is the same for dudes which start over a particular navigation default.

Setting a skill var of 10 in the ship resource means that some will go just a bit faster and others a bit slower. This works for fighters. Slow ships need to have a larger value, otherwise they will seem to be just piled up.

#15 Flares feature omitted - difficult to obtain same effect with point defence

The decoy flares feature in EV and EVO is not present in EVN. Point defence offers a more sophisticated approach to this, but has a very different look and feel. For example, in original EV, the flares were very much a low tech alternative to missile jamming. In EVN, this low tech option is not available. Conversion therefore fails.

#16: Shield Recharge values are calculated differently.

To convert from EV values to EVN values, use this equation:

( ( EV Shields / 100 ) / EV ShieldRe ) * 1000 = EVN Shield Recharge

#17: Shipyard thumbnail images generated by automatically scaling down full size, rather than being stored separately.

#18: No separate image for Hail Ship dialog.

Possible workaround: assign a .mov containing a still frame of the appropriate size as the shipyard movie, and leave the hail image in as a PICT. This will not apply to the shipyard thumbnails, however, due to #17.

#19: In EV, in-game shield values are calculated by dividing the ResEdit value by 10. For very well shielded ships, however, If the ResEdit value is specified with a negative number this will only be divided by 2.

This is unnecessary in EVN since the Shield field supports larger integers.

#20: AI ships no longer have a fuel/energy limit to fuel/energy draining weapons -- in EV it was 100 units, and I think it may have been the same in EVO

#21 Nova won't run with plugins unless it's registered

This fact is perhaps less well known than it should be — certainly if someone is thinking of putting up a 48MB plugin, they might want people to really understand that it would be a waste of time downloading if Nova was unregistered.

Also, I would expect to receive lots of 'Your plugin doesn't work' emails from people who hadn't registered.