Linear or side quests?

Depends.

Do you consider the cutscenes where Irenicus breaks free from the point of view of your character or not?

Throughout the game the identifiers of your quest are "I want revenge on a wizard who tortured me" or "I want to rescue a friend from the Cowled Wizards" which implies the designers didn't want the character to think that irenicus was loose and running the show... Yet.

Chapter Two side quests are the means of accruing the 20,000 gold for the Shadow Thieves. A practical Bhaalspawn would also anticipate the need for better equipment they can uncover (Or at least potions and scrolls) as the prison is oft described as a 'Fortress'.

Then there is the team who have their own demands for assisting you ("Of course I'll save your father, Nalia!") and a couple of situations where one is forced to work together also helps create a cohesive force.

Then there is the actual in game time and travel time. It may take longer to leave for Athkatla then come back later than to assist a town in its entirety and then leave with all the gold you can carry back to Gaelan Baels' place.

I remember playing the first time when Valen and Brus (?) approached me I was expecting a price HIKE my thoughts were along the lines of "I knew it!" smugly glancing at my 30,000... then realised I could pay both of them.

One playthrough after being given the "you'll live for a week, tops" after the soul abduction went on a suicidal spree pretty much (Also I keep mentally converting "week" to "tenday" in my head, does anyone else do that?) went around killing all the chromatic dragons, the HLEs then on the last day got wasted in the tavern, even had a little IC will Next day, woke up, got on with the quests a little sheepishly

 

The non-linearity was implemented terribly in BG2. Either you ignore the story and hug a walkthrough or you miss half the game.
For roleplaying IWD is the far better game.

I don't mind non-linearity if it's implemented properly, an example are the Might and Magic games where you don't feel bad about exploring the world.

 

I think a truly open world is pretty much impossible in a CRPG (that's what The Sims is for anyway ), so there has to be some degree of linearity. If there's a story, it has to progress. (Think fiction - beginning, middle, end, in the simplest sense.) And if a story is to progress, set pieces have to happen.

 

I'm happy with either depending on what the game is going for. Non-linear gives great freedom and an open world but linear obviously makes it a lot easier to construct a good plot and pacing. There's quite a spectrum in between. I don't like the KOTOR and Dragon Age approach. They let you choose the order of the middle parts of the game to try and disguise the linearity but I don't feel I have much freedom and it weakens the plot for those parts. Final Fantasy generally have a good system. It's very linear with good pacing but you can choose to head off on side quests if you want to. These rarely have any "story" elements though (either their own or connected to the main plot) and are mainly about getting new shiny toys. BG2 had an excellent system. Large chunks of it were on rails. The middle though was a load of side quests with their own plot and you needed to do at least some in order to progress. The timing lag doesn't bother me too much as I'm more of a completist than a roleplayer.

 

I was terrified of Irenicus when I first started BG2. While I do not consider myself a true RPer, I think going after Irenicus asap is pure suicide considering how he so casually obliterated all those high level cowled mages.
While I don't think doing every sidequest is sensible if you're RPing, you will need to do a lot of them (and as fast as possible) if you at least plan to justify that your PC is not (completely) suicidal. I guess the rest of the content was for other playthroughs, considering that you don't get to do every possible quest there is with just one character anyway (many quests are class-specific, for example).
I think it's a shame that Baldur's Gate doesn't have Diablo's content randomization engine (this was something I would have loved to see in a sequel) because I think the real reason that BG2 becomes all about the sidequests the more you play the game is because metagaming is inavoidable in BG2. It doesn't help that almost every sidequest in the game comes with powerful material rewards.
As for linear vs sidequests, I want a game which strives to have a strong main quest but still has lots of sidequests. All good games are like this, imo. Like BG gave you plenty of freedom in the beginning, but ultimately you'll find that the main quest is the driving force behind everything (it's the reason you're left wandering aimlessly for half the entire game in the first place).