1. The problem is, there is hardly any incentive for having small multiple armies over a big army.
So far people suggested,
Disease - To stop a blob from forming. Making people only make a blob when it is necessary. Also, this will probably make battle fronts wider.
Supply line?
2. I doubt you can fix the second one. Obviously people who invest more time into the game will have higher chance of victory than people who log in once a day to check things quickly.
I tire of the sticks solutions. Always the stick. Always.
"Let's make what the players do suck so bad that they won't want to do it anymore". That's what you are proposing. Blobbing is not the cheese of a minority, it's the standard of the majority. And there are many compelling reasons to blob despite the fact that blobbing has several distinct drawbacks.
The original problem is that strategy, maneuvering, etc. don't play as much a role as they should.
Throughout history, superior armies were defeated by more mobile, better positioned, etc. enemies.
While much of medieval warfare was pretty unsophisticated, from a gameplay perspective, gathering everyone in one spot and blobbing into the enemy blob is probably the most boring approach possible.
So far, disease is something I like. It also gives an alternative to siege warfare. Usually, on the brink of defeat, people will gather their army in their capital and the enemy is forced to gather a huge force outside and storm in. With disease added, they could actually besiege them.
What we need to make sure is that it's not a pure frustration moment. So it should add to attrition, and have effects that can be countered. I suggest that disease only wounds soldiers (there's still a chance for wounded to die at the turn), which can be countered with healers. It should also reduce morale. And it should very clearly say what is going on and that spreading the army out would help.
We already have starvation. What would this attrition add? If you want to make sieges better, then make it so that surrounding armies block off incoming caravans. No need for a frustrating attrition mechanic that will break the whole game. Armies can already only go so far due to morale, increasing attrition morale loss on top of distance morale loss and you severely limit how far realms can go to wage wars. Even if you split the army (which is borderline impossible if you want to go far, without adding an extra week of travels), nobody's gonna like having their troops just randomly die all the time.
In a spread out strategy, however, this is much less important. A single noble leading a unit is very well capable of seeing that a neighboring region is under more pressure than the region he is in, and move there to help the defense. Personal initiative becomes possible without completely destryoing the army's strategy. Marshals still have a role, but this role becomes more to define the tactics the army follows. Precise orders are still important, but full compliance is less important.
It's a nice dream you live in. Players, for the most part, don't like taking risks. They don't like to take personal initiative. And they generally don't like having to analyze stuff themselves.
In all of my time as general or marshal, I've often used orders such as "next turn, if X then do A, if Y then do Z, and the first to act is to report to the others". If I didn't repeat the orders based on the outcome on the next turn, as soon as possible, the rate at which the order was followed was consistently drastically lower. The vaguer the instructions, like "then move to the least defended region", the poorer the rate of deployment. Having someone take the time to analyze the big picture and willing to take responsibility for everything is extremely comforting for most players. They don't want to waste all of their time analyzing all the military data, and they don't want to assume any risks themselves.
Of course there are some like me, and probably you, who are less risk-avere and have more initiative. But that's not the majority of the player base. It's actually a dwindling and constantly more marginal portion of the player base.
Which is why I find foolish any gameplay moves that push towards strategies than rely on more active players, when there is always less of them. Finding someone willing to be a marshal or general is already pretty damn hard. Finding someone both willing to take the title and the responsibilities that come with it is next to impossible.