"Everyone missing a good chunk of active and passive skills at this point in the chapter because of a lack of SP definitely feels bad. You kind of have to sacrifice between active skill synergy or passives that you had before. And splitting up SP to get some passives and some active skills just leaves you a lot weaker and ill-prepared."
Here is the INTENDED behavior for what happens (or at least what SHOULD be happening) to your stats, skills, levels, items, and gear upon death and Reincarnation.
HOW STAT/SKILL/EQUIPMENT PRESERVATION IS SUPPOSED TO WORK (For The Immortal Shadow)
When you die , you lose 1 level and most of your skills. When you Reincarnate, you gain +50 jp to spend for each level beyond your first. Your AP allotments should persist. HALF of any RESOLVE loss/INTELLECT gain from learning spells should persist (a last minute balance change was made to change this from all to half, because I got tired of Reincarnating in a new Vessel with a starting Resolve score of like 3 because I had stupidly learned like every spell possible as the last Vessel, and thought players would tire of this too, even if the obvious fix for that playstyle (OF MINE!) is 'maybe don't cram EVERY SINGLE SCRAP of FORBIDDEN KNOWLEDGE you come across into your skull, genius'). Skills learned from the Egyptian Pantheon or other "special" means should not be lost when you die and Reincarnate (if you bought Blessing of Bast through the Learn Skills menu, it will be lost, but if you received it from Bast herself in Egypt, you'll still have it).
In the seven weeks since the last round of pre-alpha development and playtesting, I have legitimately forgotten what happens to your spells upon Reincarnation.
When you die, you lose all of your equipment and items. When you reincarnate into a different Vessel, you receive bonus starting cash based on your Reincarnation Count. For Checkpoint A1, for instance, this is Reincarnation Count x $250. If you reincarnate into the SAME Vessel, you receive that bonus cash, plus ADDITIONAL bonus cash based on your level. For Checkpoint A1, for instance, you receive ADD'L bonus cash equal to your Level x $250. So reincarnating into the same Vessel (say a Level 10 Academic) at Checkpoint A1 with say 2 Reincarnations under your belt, you should have bonus cash of $3000 ($250 x 2 Reincarnations + $250 x 10 Levels). This money can be spent at the Bazaar to get you closer to the power level you were at before you died, but also lets you experiment with new items and equipment.
HOW LOOT POINTS AND REINCARNATION ARE SUPPOSED TO INTERACT
Any loot you collect from an area in the same Investigation will NOT respawn when returning to that Investigation (irrespective of Vessel). This is by design. Instead, depending on your Reincarnation Count and some other hidden factors, new, weirder, and better loot may spawn in the previous areas. This is meant to enhance replay value, a concept I think comes into play in EREWHON well before you actually clear the game.
So zutsu13, what this boils down to is that the answer to your issues with feeling naked and underpowered upon Reincarnating as the Academic on 2F can be rendered in a single word: Bazaar!. You should have noticed that you Reincarnated with a fair bit of cash to a TON of cash depending on your level. You also should have some of the items Malphus will take to open a portal to the Bazaar in your inventory, if you are the Academic (didn't give the Occultist this grace, I think, because he can MAKE those items). Even if not, I believe that when you Reincarnate to this checkpoint, Gabrielle's equipped weapon will also pay for opening the portal. So, go through the portal to the Bazaar, and gear up. (Don't accept the Mad Arab's gift lightly, should it be offered.)
Unless of course there's another bug that I didn't see on my last pre-alpha playtesting runs: always a very real possibility!