I don't think anything needs to be changed as far as the story structure is concerned. Add a new villain and keep everything else as is - specially the humor - then we are good to go.
That said, the Shadowgram is 1 of the best customization systems I've ever seen and I have some suggestions to improve and fix some game mechanics. Wall of text Ranger!
1-) Stat Boosters (ie: LAT Booster, etc) should only take 1~2 tiles in the Shadowgram (except HP Booster) otherwise they become obsolete pretty fast, sometimes even before you actually acquire them. Or remove them from the game (again, except HP Booster).
2-) Create a new Mod Plug that negates Condition decay while using specials. Size: 3x3 and variations (total 6 tiles), comes in different types for each equipment (Head/L Arm/R Arm/Legs/Expansion).
3-) Create a new Mod Plug that decreases Condition decay while attacking to 0 if and ONLY IF that part was NOT used to hit the enemy. Size: 2x2 and variations (total 4 tiles), comes in different types just like the above. This is mainly to fix the usability of certain equipment like many Heads/Legs/Expansion that lose Condition while attacking but it also allows 1 to use most L/R Arms for their skills/specials only as long as they don't regular atk any enemy directly with said Arms equipped. As it is right now, players refrain from using aesthetically pleasing favorites just because of this arbitrary decay and customization greatly suffers from it for no reason.
4-) Change the effect of all "Capsule" type Mods to allow one to save what is currently equipped too instead of choosing what to save only from the Pouch.
5-) Change the effect of "L Container" to Pouch capacity +7. As it is, it's almost never worth using it over M Container.
6-) Change "Chip Up" effect to give +2 to surrounding chips AND make it so Hero Energies can pass right through it. Or remove it from the game.
7-) Increase "Unlosing Boost" Mod Plug to give at least an increase more similar to +20% (or decrease in 20% of enemy kills) and +20% per Hero Energy.
8~) Change "Frugal Eater" Mod Plug effect so it adds +5% chance per Hero Energy to retain items after use.
9-) Change "Pharmacist" Mod Plug to give +25% effect for healing items. Keep that +5% per Hero energy as is.
10-) Create 1 generic weapon (non Dengeki) of the "Other" category that only goes up to Rank 5. This allows 495% at max Condition with "Other" Dengeki weapons at expense of % stat bonuses compared to other ranged atks that can go up to 694% (so it becomes an unique weapon type with pros and cons). As it is, "Other" weapons are just bad and not sustainable.
11-) Create or change 1 generic Gun type weapon to have range 3 (even at Rank 6) and Condition cost of 3% per atk. There's no reson NOT to, considering certain L/R Arms have range 3 and 2% Condition cost, at which point the only unique factor to Guns is the Sharpshooter skill (100% HIT rate) which also requires 1 R Arm part. Because of this, the Condition loss of this combo isn't sustainable even at max Blacksmith and max Caravan for repairs (however, this Arm decay is also fixed by suggestion No.3 on this list). Note: while a cost of 3% is just on the verge of not being viable, suggestion No.2 makes sure this works (via Specials).
12-) Create or change 1 Dengeki Staff type weapon so it takes 3% Condition per atk (as opposed to 4%). Same reason as the above, 4% isn't viable.
13-) Change Staff type weapon regular atk range to 1 diagonal in all directions simultaneously*. This is to justify their costly Condition per atk (unsustainable 4% or barely sustainable at 3% with my suggestion No.12) while also giving them some unique strategical flavour. *It doesn't have to be precisely like this (diagonals), it's just 1 example in order to make their regular unique and useful as opposed to obsolete.
14-) Increase "Human Driller" cost to 2% Condition per atk.
15-) Change "Desperation" effect to +4% damage per Hero Energy, increase the default effect to +30% damage.
16-) Decrease "Helping Hand" skill cost to 4.
17-) Decrease "FOV Expand" skill cost to 2.
18-) Change "Bushido" effect to add +1% damage per tile of Hero Energy. Crossing multiple Hero Energies doesn't offer more bonuses per tile but using different unfused energy as multiple streams still works.
19-) Change "Inorganic Food" and "Organic Food" skills to reduce 2% Condition cost per Hero Energy when you eat some equipment through their ability.
20-) Change "Mana Release"/"SAT Boost"/"LAT Boost" to skill cost 4.
21-) Change "Sleepy Jelly"/"Confuse"/"Poisoning"/"Paralyze"/"Sleep"/"Forget" so status infliction increases with more Hero Energies.
22-) Change "Star Aura" effect to -20% damage from Humanoid and Boss enemies (can't stack other Star Aura skills).
23-) Change "Stomping" skill effects so they only disappear when an item drops and the effect doesn't reset if you take other actions, it just won't increase if you do.
24-) Keep "Practice Swing" to +5% boost per swing but change its Hero Energy cap bonus to +25% per energy.
25-) Change "Auto-Charge" so its effect doesn't disappear when moving to the next floor, only when a Special is activated.
26-) Change "Berserker" effect so atks and specials will either be criticals or deal 30% less damage instead of missing.
27-) Change "Devour Enemy" skills so copied skills only disappear when another skill is copied instead of disappearing when you move to the next floor.
28-) Change "Count Shot" so its effect only disappears when you atk an enemy instead of disappearing when you do any action other than moving, when you get atacked or when changing floors.
29-) Similar to above, change "Count Block" so its effect only disappears when you take a hit (natural misses don't count).
30-) Like above, change "Count Step" so its effect only disappears when an enemy attacks you (regardless of hit or miss).
31-) Like above, change "Count Attack" so its effect only disappears when you atk any enemy.
32-) Change "Warrior Tribe" so it consumes 10 Energy instead of consuming the item with this skill. Does not activate if there isn't enough Energy.
33-) Change "Shadow Dance" Hero Energy bonus to +5% per energy and make sure it stacks with "CQC Evade" and "Ranged Evade". This would allow 100% evasion for either SAT or LAT attacks but not both at the same time.
34-) Change "E Force" to +20% damage to Elemental atks. Keep that +2% bonus per Hero Energy as is.
35-) Change "Head Wind" Hero Energy bonus to +3% per energy.
36-) Change "Light Shadow" so it can stack with Silent Kill.
37-) Change "Seduce" to +50% damage. Keep the +5% bonus from Hero Energies.
GENERAL SYSTEM CHANGES:
38-) Change the Special Cast/Activate system so it's possible to use Specials while Unlosing Modes are filled and ready to use.