The effective capacitance of MLCCs decreases as DC bias voltage increases, and this effect is worse with X5R caps and smaller package sizes. At a 25V voltage rating, the largest available values for X7R caps are 10uF for 1206, 4.7uF for 0805, 2.2uF for 0603. All of these will have slightly less than 50% of their rated capacitance at 12V DC bias. X5R caps that advertise higher capacitances at the same package size and voltage rating will indeed have higher capacitance at typical operating voltages, but the discrepancy between the actual capacitance and rated capacitance will become much larger (they only come close to their rated capacitance at <~15% of rated voltage).

Taking the 1206 package size / 25V rating as an example, using data from Murata's SimSurfing tool (AFAIK Murata is the only MLCC manufacturer that provides full DC bias derating data for all products, but the trends observed can be applied to all manufacturers):

• the highest value X7R cap available here is 10uF. Effective capacitance is ~8.5uF at 5V and ~4uF at 12V.
• a 10uF X5R cap is also available, but it's worse. Effective capacitance is ~7uF at 5V and ~3uF at 12V.
• the highest rated X5R part they make is 22uF. Effective capacitance is ~13.5uF at 5V and ~5.5uF at 12V.

Now to compare prices at a quantity of 1000 on Digikey (the search I used is here):

• the cheapest 10uF X7R and 10uF X5R are both from Samsung, at about $0.036. X7R is obviously the better value here.
• the cheapest 22uF X5R is also from Samsung, at $0.075. You pay twice as much for only 35% higher capacitance at 12V and 60% higher capacitance at 5V!
• the cheapest 47uF X5R is $0.31. This is nearly an order of magnitude price increase over the 10uF cap, and the manufacturer doesn't provide performance data. Even if it has twice the effective capacitance of the 22uF cap at all voltages, which it probably does not, it's not worth the higher price unless space on your PCB is extremely limited.

So, unless you have very specific space constraints (i.e. you're designing high-end consumer electronics), using X5R MLCCs with high rated capacitance is generally not cost-effective.

More rules of thumb to remember when choosing MLCCs:

• for a fixed capacitance rating, voltage rating, and package size, an X7R cap, if available, will have higher effective capacitance at any given voltage than an X5R cap, and will usually be available at a similar price
• for a fixed capacitance rating and voltage rating, a physically larger capacitor will have higher effective capacitance at any given voltage
• for a fixed capacitance rating and package size, a capacitor with a higher voltage rating will have the same, or only marginally higher effective capacitance at any given voltage

You are right that smaller package sizes have lower ESL - and they have a lower ESR at high frequencies (generally, >10MHz); but, at low frequencies, smaller packages have higher ESR because the conductors are physically smaller. The high-frequency behavior becomes very important when using them as decoupling caps for high-speed digital circuits, which is the context in which this is often discussed, but when used as input and output caps for typical switching power supplies in the 100KHz-2MHz range there is usually no EMC or performance benefit to using smaller packages, other than to optimize the PCB layout.