Version differences
There are two versions of TFTD. The original unpatched version of TFTD and the one with the v2 update.
Players with the Collectors Edition of TFTD have the version with the v2 patch.
The known changes in the research tree are as follows:
Unpatched
A Lobsterman Navigator is needed to research Magnetic Navigation
Ion Armour is not required for Magnetic Ion Armour. All the technologies you need for Magnetic Ion Armour are Plastic Aqua Armour, Ion Beam Accelerators and Magnetic Navigation.
v2
Magnetic Navigation can be researched as soon as one is in storage. The lobsterman navigator is NOT required.
Ion Armour is required for Magnetic Ion Armour. Magnetic Ion Armour now just requires Magnetic Navigation and Ion Armour.
Yes, in other words, the v2 patch makes it easier to get Mag. Ion Armour. However, it also means that winning the game hinges on your ability to obtain a live Deep One terrorist AND researching it in the right order.
If you patch your game and reload a campaign created before the patch, you might face a few research problems. It's not that common, but you might find that you'll have some trouble with researching the more advanced armour via the V2 method. There should be no problems if you haven't even started on the Ion Armour or Mag Ion Armour yet. It's mostly for campaigns where you're already half-way through researching the armour.
v2.1
Only difference from v2 (per StrategyCore) is that the MC Reader bug is fixed: it can be research even if you didn't have a sample when MC Lab was complete. Note that TFTD CE is v2 and does not include this fix.