These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
That One Boss: Sanae in You is by far the toughest boss you'll face until the Final Boss. Her Miko innate skill gives her a great boost in Accuracy and Evasion, meaning that she will be able to hit even your dodgiest of units while your own struggle to even touch her. Her attacks are very powerful, and the special effects of her spell card can be debilitating. "The Day the Sea Split" will treat all attacks against Sanae as though she were standing in water, which largely means that they will do diminished damage. "Summon Takeminakata" gives her the spirit Focus auto-cast every turn, which will boost her already insanely high evasion and accuracy even higher. Finally, her final spell card is a MAP attack with a large range... and she casts Miracle after declaring the card, which gives her nearly every buff in the game. If you don't manage to take her out in a single turn or get all of your units away from her, she can easily cause a Total Party Kill. She's a tough nut to crack even if you go into her battle prepared. Those who aren't will most likely get their asses kicked quite handily.
Not surprising as she appears to be the favored character of the designers, possibly overlapping with Creator's Pet as she has perhaps the best animations and her 3rd special skill? SP Regen with a remark about her being the developers' "Waifu" in the notes.
Scrappy Mechanic: How the second game handles units: the stronger the unit the higher its "cost" and each mission only gives you a certain total cost. This alone wouldn't be so terrible if not for the rather large number of characters by the end of the game. This might have been done with good intentions (namely stopping players for fielding only heavy hitters), but there's usually good reason why certain mechanics are not in normal Super Robot Wars games (closest thing would be how Alpha 3 handles its 4 unit squads, but it has no bearing on the total number of squad deployment)