The game still feels rather linear, at approximately 10 hours in. Yeah, I have a lot of active quests, but I still feel extremely limited in where I can go. The galaxy feels significantly smaller than it did in ME2. I feel much more like I'm on rails, playing a typical shooter-type game that already has a pre-determined plot and direction with no choice, like Halo or Gears of War or something.
Also, I'm feeling like there aren't nearly as many choices to make. Most of the places where there would have been a dialogue option in a previous game (even if it's just something simple like an "Investigate" menu), there are now mini-cutscenes that play a pre-determined response from Shepard based on your past choices (like they did in DA2, where if you typically play a jackass, the auto-response is more harsh, but if you typically choose humorous responses, the game might fill in the auto-response with a sarcastic joke). But even then, where there are choices given, I feel like they're not even really a choice. See "Plot spoiler" below for example. I get that there's supposed to be this sense of desperation and enormity about the game. But, I just feel like they removed the heart of what made the choices so interesting and powerful in this series and left the hollowed-out shell. You get "Yes" and "No", but there's no more "Why?" like there used to be. You get "Destroy it" or "Save it" but there's not a "How do you feel about it?" dialogue to accompany it to give you more information, or to put more weight into the decision.
Now, as for the space-probing thing... It's hit or miss with me. On paper it sounds like a great idea, but it just gets frustrating only being able to scan a system once or twice before the Reapers come a-knockin'. Not that I expect to be able to gather everything in one pass, but some of these systems are pretty large, and the scan only covers a fairly small fraction of it. Having to go back and scan it 6 or 7 times is annoying, especially considering I forget where I've already scanned half the time, due to needing to go and play a mission to clear the Reapers out from the system pretty frequently. But, then again, I was never really a fan of the scanning thing from ME2, or the Mako missions from ME1, either. So maybe this is just one of those areas of the game I'll never really like no matter what.
Now, despite all the negative stuff said above, the game is intense. Combat is fluid, the AI can be challenging, and the different enemy types do a good job of forcing you in to different tactics and mixing things up. It's not always a game of finding cover and shooting until the enemy dies (though there is still a lot of that). There are now enemy types that charge your position and force you out of hiding, enemies that cannibalize the corpses of those you've already killed to regain life and shields, enemies with literal riot shields that you need to find a way around (which, as a Vanguard isn't too bad, but some classes will have trouble with these guys). There's also a much bigger emphasis on team coordination. In ME2 it was pretty important, but there were only so many ways you could combine powers. Here, it seems like every ability has some kind of synergy with something else, which means you're mostly free to pick and choose who you want for each mission. With all the new additions to the skills and powers (and the ability to respec everyone!), there's really no limit to what kind of combination you want. Warp and Warp Ammo react wonderfully with Singularity, Pull, Charge, and many other powers, and it's a beautiful sight. Yanking someone to you with Pull, freezing them with Cryo from another party member, and then watching them shatter as they hit the floor when Pull wears off... it makes you wonder how people have been playing games like this without this kind of fluid interaction and seamless coordination.
I also LOVE how they handled cooldowns. I tend to only walk around with two weapons, so I have a -196% cooldown timer, which is amazing. I can use Biotic Charge every 3 seconds, and it's beautiful. Charge in, shoot an enemy or two, use Nova to knock people away, then charge back in to the next group to recharge my shields and reset for another Nova. It doesn't always work, since some enemies have pretty powerful armor and shields, but on most groups it's wonderful.