I guess I should also say that Star Wars Rebellion is the highest Star Wars strategy game on their list.  If you are looking for a Star Wars strategy game, then I highly recommend it.  You can, among other things, create your own Death Star and destroy planets.

A few years ago I played Master of Orion for the first time.  I really liked it, but for some reason I really prefer to control ships from the Star Wars universe.  I guess I should try Galactic Battlegrounds within the next year and compare it to Rebellion to see which I like better.

48. Metal Slug 5?
41. Warlords 1?  (It's the only Warlords game I've played and it's been a while.)
37. Game Dev Tycoon

Here are some more clues:

38. This game is the first time a single player game in this series showed the monsters that you fight in the overworld before you encountered them.  Consequently, people said this game felt like a MMO.

37. This is the first time this popular video game series featured 4 player co-op.

36. SNES games had significant size restrictions, but this game effectively doubled the size of it's overworld via a clever storytelling idea.

35. The title of this game is also the title of a movie.  The movie is also the #2 top grossing movie in North America for its release year.

34. The title of this game references a city in a popular fantasy world.

#38: Final Fantasy XII

#37: New Super Mario Bros. Wii 

#36: Could be many games The Legend of Zelda: A Link to the Past, Final Fantasy VI come to mind.

Galactic Battlegrounds is a very basic, on the ground strategy game; build a town hall, train workers to mine resources, build baracks, train soldiers, advance tech. There aren't really any ships to control, besides some air units. So while that stops it from being really epic like the stuff you describe above, it's mindlessness is a lot of fun. It also has a fun campaign mode, with missions for every faction (except the Naboo) taking place in the background of Episode I, II (with the expansion pack Clone Campaigns), IV, V and VI (no III sadly because it was released before that movie, and unlike when II released it didn't get another expansion).

Bold: That is an enticing reason to try out Rebellion.

All three are correct.  #36 was Link to the Past.

Football Manager?

Nope to all 3

Metal Slug and Warlords are the right IP, but it's the wrong game of the series for both.

48 - Metal Slug 3

#48: One of the later games for the Neo-Geo, but also one of the best - and certainly the best of it's series

Hint #1: The run&gun series is well known for their hilarious and top-notch sprite animations.

Hint #2: In this remake of an early title of this series, you first fight through an army of soldiers, but end up fighting off an alien invasion halfway through the game.

Hint #3: The series has already been found out before, (Metal Slug), but not the correct title yet.

Hint #4: It's not Metal Slug 5, as had been repeatedly guessed.

#41: Greetings, Warlord! Let the war begin!

Hint #1: This is an old turn-based strategy RPG, but the series got more known later on for their RTS spinoff series.

Hint #2: As has been found out already, the game is from the Warlords series. And this one has a Deluxe version.

#40: A very unusual RTS in space, where you start with a small capital ship and 3 planets to govern, but the map (and thus the number of planets to govern) and fleet grows at specific points in the story when you reach a new rank.

Hint #1: You start this game with your main planet almost in ruins, with most buildings massively damaged.

Hint #2: The Alien factions make war independently from you, even way before you have even the rank and thus ability to contact them, quite possibly eliminating some races before you ever had the chance to meet them.

#38: A PC-exclusive Pinball game with a horror theme.

Hint #1: Tables are a haunted Castle, a Dungeon, and Frankenstein's Laboratory, complete with the Monster in it's center.

#37: Bring your console-making back from the brink of death by hiring 2 kids and beat your programmers into submission in RPG-like combats.

Hint #1: This game came out shortly before the company making it stopped making consoles for good, making the premise highly ironic.

#34: A Top-down building game where all you build is just one specific structure - but with everything that it entails, like walls, rooms, kitchens, yards, power and water supply, and so on. Prison Architect, Jail time for Peelman