My most recent main story mission was Priority: Palaven. Since then, I've been doing as much side stuff as i can. So, after exploring the Citadel i got like 10 new missions added to my journal. Now, some of these missions show up on my galaxy map, such as scanning for artifacts on kate nash or whatever, but a lot don't, like finding out what happened to that senator's son. So my questions is this: Am i just not far enough in the story to see the places these missions are in, or am i supposed to guess and check where the hell Irune is?

I also don't like that it doesn't tell you what you're supposed to be doing next for the mission like in ME2.

TL;DR: Do missions show up on my map like they did in ME2, or not?

A lot of the minor side missions don't IIRC. You just have to be vigilant and keep an eye out for any new Mass Relays that might appear. I missed something like 3 side-quests and 5 systems worth of planets because I didn't realize a new blip had appeared on the Galaxy Map.

It's kinda annoying so just keep your eyes peeled.

Also check the specter shop after each mission, some of the items needed for side missions are gotten there.

Just keep playing and if they don't show up, you're either not able to find what you need yet or you've missed it (in which case just check the Spectre store as mentioned where they'll show up to buy).

Both the journal and the galaxy map kind of sucks massive ammounts of ass, so just write down every name there is to find in your missions. Most of them are just scans anyway.

Also, don't care about the reapers coming. Just hit and run (enter, fly through scanning then leave and repeat) if they come, and you'll find everything. Don't be afraid to get caught, it's just a minor setback.

Dude, the side stuff is really easy. At first you'll wonder why it's made confusing, but all you have to do is go to every available system and scan what needs to be scanned until you get 100 percent assets, then leave, go back to the citadel, check your map and see if there are any new names on the map, if not, go check the spectre terminal in the embassies, if you can't update the side quest before the next main mission, you'll know it's because you can't do it yet. The mission you want to do, the senators son, is a side mission on another planet which should come up at some point in time. I wouldn't say that it's all laid out perfectly, but it's good enough that you'll be able to easily do all the side stuff before the end game. Just make sure you scan everything possible and check the spectre terminal before going to the main missions. Also, it doesn't always happen, but some side quests will confuse you because there's a bug that just makes the mission not able to complete. I didn't have it happen the first time through, but on my second, it did. The whole side missions aspect of the game is such a chore to make the game longer, and the only reason you may not completely notice that the first time is because you'll be so into the story not to care.