Now my thoughts:
1st off - my opinion is that this is the best game ever made. period. 80hrs in, and I am still having a blast. However, I do believe it is lacking in certain areas which could be improved.
I think it's close, but it's not there. Have you played Baldur's Gate II? It came out in 2000 and I still think it is the best RPG ever made.
If Bathesda would make some changes to their approach, their next game could easily be the greatest game of all time. I believe that in they probably look at a lot of these suggestions and think "well obviously our approach is better, it's working - our games get more popular with every release." This line of reasoning is no good. Yes their games get better, and thus more popular every time. That doesn't mean that the things they do the same in every game are necessarily good, or the best that they could be.
Here are the two major things that I think could be changed, and make their next game the best of all time.
NUMBER ONE:
Revamp the character development, or "class" system. As it stands, I think that this is one of the weakest parts of their games. Their development system appears to be part of their theme of freedom of choice. I get it, but I don't think it's well executed. As it stands, there really aren't all that many choices to be made. While the perk system was a HUGE improvement, there is still a lot of ground to cover.
Firstly, there aren't that many different play styles available under the current system. You can be a spell caster, thief type, or warrior type. Of course there are a lot of variations within these three archetypes, and there are hybrid types possible, but unfortunately these variations and hybrid classes really don't offer much difference in play style. The three primary archetypes offer three different play styles, to be sure. But, there isn't much difference in play style between one thief and another, one caster type and another, one warrior type and another.
As a caster, for example, it's going to be pretty much the same every time. The only difference is you might shoot electricity instead of fire, or frost. The problem here, is two-fold. First, although going to a set spell system instead of a spellcrafting system was a HUGE improvement, there aren't really that many different types of spells. So, while playing a mage is easy, playing any other type of caster is impossible. You want to be a druid/ranger type character? Sorry, you can't shapeshift (absent catching a disease, but that doesn't count it's not a class ability), you can't summon animals/plants, you can't cast any nature oriented spells (like track animals, conjure food or whatever you can think of from the traditional druid canon). Want to play a cleric? Well the restoration school is pretty awesome for this class (despite the lack of any heal over time spells), BUT, you can only summon evil daedra, not very clericky, and there are no real combat buff spells available which is a big problem for a cleric (buffs that add damage, fortify abilities, stats, etcetera). Second, even if there were a lot of spells, you aren't ever locked into using any particular set of them over another. So, you'll just use the best destruction ones every time, and ignore the ones that aren't so great. The same is true for every school.
On paper this system makes it seem like you have tons of choices, and you do - you have tons of relatively trivial choices that have no major impact on play style. The only major choice you can make is to NOT take certain perks and gimp yourself. So, you get those perks every time, and end up with the same character every time. Now here come the people saying "it's your choice to take those perks every time!" Well yea, that's true, but why would I NOT take the perk that halves the magicka cost of the spells? That would just add arbitrary, boring difficulty (as contrasted with fun difficulty) to the game. It wouldn't change my play style it would just make it harder for me to kill things with the same spells.
So, suggestions? Go with a class system where you are locked into certain ability sets from the beginning. Give us a wide range of choices. People want real choices. I want to choose a race (where each race has a really good racial ability setting it apart from the others - like histskin or high born), a birth sign, and a class that offers a varied playstyle from the others. In D&D for example, if you went with a Cleric you then got to choose two domains that offerred various special abilities or spells. That was cool, and that's what people want to see. Interesting class features that make playing one class over another meaningful.
Give us a wide range of meaningful choices, not an infinite range of trivial choices ("Well on this character I had 250 stamina, but on this one I went 270 stamina, so it's totally different." No, it's not, it's the same thing).
NUMBER TWO:
Spend more time and money on the story, the dialogue writing, and most importantly VOICE ACTORS. Lots of them. They don't have to be famous. Instead of spending a huge chunk of cash on getting Captain Pricard and Agent 006 to do the voice acting, just hire cheap no-name actors instead. No point in spending the big bucks on a famous voice.