Here’s something you could try. For ease of play, give all attackable neutrals some set ipc/production value. I would suggest 1 ipc if you want to avoid introducing more potential factory locations into the game, or 2 ipcs if you do want the factory option. But pick a generic number and make all neutrals worth the same amount (this is so you don’t have to find a way to graphically represent different ipc values for each territory on the map.)
Then to differentiate between these neutrals, use neutral standing armies. For this you could use chips or some of the inf sculpts you have left over from classic. The gray Germans would probably work well for this since they are unlikely to be confused with any of the colors from 1942.2.
Any neutral territory that doesn’t have chips/infantry on it, is considered impassible. Place an upside down control marker on those territories.
Those that do have armies (and no upside down marker) are considered attackable neutrals.
Attackable neutrals cannot be flown over, they have to be conquered first. Once conquered they behave like all normal territories, in play at whatever generic ipc value you chose for all neutrals.
This way it’s easy for your players to know how much a neutral is worth (all the same amount of ipcs, whether you go with 1 ipc for all, or 2 ipcs for all) and easy to tell at a glance how difficult it will be to conquer, since you can see the standing armies.
This might not be perfect from an historical accuracy standpoint (all neutrals at the same ipc value) but it will be expedient for the gameplay, since those numbers are difficult to change without drawing on the map. The standing armies allow you to adjust the “difficulty” of attacking any particular neutral. So a strategically useful territory like Spain, Turkey, Afghanistan or Mongolia might have a sizeable standing army say 10-12 neutral infantry. If using actual sculpts instead of just chips, you could create more interesting standing armies, perhaps with neutral fighters or tanks to provide some extra defensive support. A somewhat less strategically useful territory like Sweden, Switz or Saudi Arabia might have like 6 neutral infantry. Out of the way neutrals that are harder to contest with large scale attacks, or distraction territories (like those in south America, Mozambique, Angola, Eire) might just have 1, 2, or 3 inf.
Then you just make a little neutral set up card, with the appropriate standing armies and impassibles listed in a chart, to fit whatever gameplay dynamic you’re after.
This gives you a way to vary the “potency” of any particular neutral, via the standing armies, without having to assign them all different ipc values. And it gives a way to quickly denote which territories are impassible, with the upside down control markers.
If you really want to adjust the individual ipc values of each neutral territory, this is possible as well, but requires that you create a special marker for the purpose. HBG sells some markers that might be useful for this, you might repurpose the markers for aircraft range, for example. Probably you’d only need markers for 1, 2, or 3 ipcs, since anything higher would likely be overpowered. As of yet, I’m not aware of anyone who’s attempted to get neutrals into the boxed game, though there is a tripleA game called Big World 1942 that uses the attackable neutral concept. It’s a somewhat larger scale map, with more neutrals than 1942.2 has, but you might want to check it out for some ideas.