Some more clues to my games:

43.  a) This entry in the series can be seen as connected to the first entry in a variety of ways.
b) One way this game is connected to the first entry is that they have the same final boss.
c) One way this game is connected to the first entry is that they both have an overworld with much of it open for you to explore from the beginning.
d) One way this game is connected to the first entry is that it returns to a top down perspective.
e) Yet another way this game is connected to the first entry is that in both you must save the titular princess.

41.  a) The premise to this game is the same as the Neverending Story, which is ironic, since this is a spinoff of a series that has the opposite meaning.
b)  This is a Gameboy Advance title.
c)  Sequel to a game on the PS1.
d)  It's a tactical RPG.

40. a) The source material for this game is classic Chinese literature, but it is not any of the games from the "3 Kingdoms" era.  First in the series.
b)  If the title of this game were translated to English, it would be "The Water Margin".
c)  The plot of original Chinese literature was about a group of bandits from the marsh.

38.  a)  The premise of this game is that you must pay off a debt to an unsavory character.
b)  It's a run and gun in most levels.

Could this be A Link Between Worlds?

41) Final Fantasy Tactics Advance?

More hints:

40) Prisoner's Dilemma

999 -> 0

39) Though the game has no combat you can wield an axe and bring it with you suprisingly far

You can also paint QR codes with buckets of white paint (which is weird since a lot of it is black)

38) There's two of you and both become party members

A JRPG for the PS2 and later 3DS

37) The owls are not what they seem (again)

The combat was completely redesigned from the first game, it makes for great gameplay but does feel a little strange given the main character

43. Legend of Zelda: A Link to the Past

38. Cuphead

39. DKC 2: Diddy's Kong Quest
I don't know what Rare was on in the late 90's but they need more of it. DKC 2 was everything the first game was, but better. The levels were inventive and clever with graphics that were some of the best at that time. The secrets and mini-challenges were plentiful and so were the animal companions, Squitter the spider being a favorite of mine. Best of all was the soundtrack. David Wise was at the top of his game and gave us an OST that was great all the way through, altho Stickerbush Symphony has to be the stand out.

#39 includes this AI companion, a future version of Siri/Alexa

Close, but no

41 Correct!

Both correct!

The phrase "connected to the first entry" essentially meaning "linked to the past".  Good job!

The next batch of hints.

#35

-Elder Crossing

#34

-Lord of Calamity

#33

-Each kingdom stands in ruins, their kings long gone, but the queens still remain

#32

-The main character becomes a teacher at a military academy after being a student in the previous two games

#31

-A journey for revenge brings little else beyond death and misery for everyone involved

Here are some more clues to my games:

40. a) The source material for this game is classic Chinese literature, but it is not any of the games from the "3 Kingdoms" era.  First in the series.
b)  If the title of this game were translated to English, it would be "The Water Margin".
c)  The plot of original Chinese literature was about a group of bandits from the marsh.
d)  In the game this literary group is represented by 108 different characters.

37.  This is the first single player entry in the series that does not have a separate battle screen.

36.  The is the first home console entry in the series to feature local co-op.