I have been playing SE4 on and off for years and GC2 for, well.. 2 days, and I recommend you to get GC2. This is why:
* AI. For SE4 to be even mildly challenging you will need to get mods, and it's still not very hard and you have to give the AI bonuses (It is in part due to the warp point structure of the strategy map in SE4, players can easily block a warp point with mines and satellites to prevent anyone from entering, I have NEVER lost a planet to the AI once I have set up defenses on the warp points). GC2 seem to have a much better AI, but I haven't played long enough to comment...the AI does seem to respond to your decisions, unlike in SE4 where AI players seem to be completely idle sometimes. This is a severe limitation to SE4 because the AI could act pretty good sometimes, then towards the end of the game suddenly stops responding to anything you do...the feeling I had when playing SE4 was always that I was actually hoping the AI would send ships to attack me, just so I know it didn't go brain dead on me.
* Ship designer! SE4 is really ugly, and you'd have to download shipsets for it to look less like a spreadsheet. GC2 looks great IMO, ships and maps are in 3D and you can design how they look..really cool feature if you are hardcore.
* Speed. Although SE4 is 2D and uses spirtes and all, it seems it's much slower than GC2. Turn calculation is longer and if you fight battles tactically (you would want to because the auto-resolve feature behave strangely sometimes), and have carriers and fighters, a single tactical engagement can take up to an hour. It is because of this I have never actually finished a SE4 game, it gets really slow towards the end when everybody has alot of units.
* Visuals.. SE4 is really ugly. I know this is to most the least important factor for strategy games, but SE4 is so ugly with amateur made graphics I felt the game would be better with just text. You can, though, download shipsests, some are quite good, but it takes a lot of time finding and installing them and hard to have a consistent style in your games because they are made by different people.
To SE4's credit, some aspect are better than GC2, depends what you want. For example SE4 has more detail in some aspects, such as it records the performance of a class of ships you designed.. it allows massive battles and it has carrier fighters etc. It also supports PBEM although I've never tried..Ship design has a lot of details and different components such as ECM and ECCM and Cloaking etc.. SE4 being years old also have a lot of mods and image sets, some such as the TDM mod made the game a lot better and can change the game play in drastic ways. Though with GC2 selling a lot more copies and also (it appears) very moddable I think in time it will also have great mods.
SE5 is in development by the way, so maybe the next version will be able to compete with GC2, for now, you should go for GC2. And if you do get SE4, get the mods, the game is nearly unplayable and too ugly without them,