1.) It is mathematically better, for Shoes of the Magi, you're paying: 1500 Gold
for: +45 Magical Power +10 Magical Penetration +18% Movement Speed
For Shoes of Focus, you are paying: 1600 Gold
for: +30 Magical Power +15% CDR +250 Mana +18% Movement Speed
2.) With items like Book of Thoth and Spear of the Magus becoming more prominent and used in the current META, the value of Shoes of Focus rises due to Book of Thoth's passive. Which is: You permanently gain +10 Mana per stack, and receive 5 stacks for a god kill, and 1 stack for a minion kill(max. 75 stacks). Additionally, 3% of your Mana is converted to Magical Power.
When I did the math, spending a total amount of 4,150 Gold , you gain: +160 Magical Power
(this amount does not count scaling mana you get from leveling up) +1,000 Mana +15% CDR +15 MP5 +18% Movement Speed
Now, keep in mind that Gold in SMITE comes by fairly easily, so 4,150 Gold is a piece of cake.
Conclusion
So, that's pretty much my side of the argument. The reason Shoes of Focus is better because the deduction of mana sustain on Shoes of the Magi, is not worth the +5 Magical Power that it gives.
Depends on the god you're playing and what you prefer. For the most part though, Shoes of Focus are the better choice except on gods like Scylla, Ao Kuang, Freya, etc.
I have to say I'm a little confused about the fact that you (imo) don't properly back up some of the claims you make.
1) Saying something is "mathematically better" really doesn't mean much without the numbers to back it up, which is why it seems a little odd to mention that after declaring you haven't done all the math yet :P
Alternatively, you may have left the numbers out since you said at the end of your post that the difference in Magical Power between the two items is 5 instead of 15 and therefore thought doing calculations was unnecessary. Either way, it's important to determine how much gold a difference of 15 Magical Power and 10 Magical Penetration translates to and how that compares to the CDR/Mana from Shoes of Focus.
However, there's one tiny problem when trying to do this: as far as I know, Hi-Rez hasn't actually told us how much every stat in this game is worth. As such, the best way to get an estimate value is to do calculations based on the stats and gold costs of some of the base items, but even that is a nowhere near perfect method. After all, every item in the game has its own "gold efficiency ratio"; some provide exactly as much as you pay for, while others are (slightly) more efficient or inefficient. For example, without even doing any math, it should be clear that using Magic Focus to determine how much 15 Magical Power is roughly worth would lead to a completely different outcome than the more gold-efficient Soul Reliquary, which provides more Magical Power and extra Mana for an overall lower price.
On top of that, some of the other users in this thread have already rightfully pointed out that other factors influence an item's value as well. If your God has such high cooldowns that you'll only be able to use one spell rotation per teamfight, amplifying the damage of that rotation will always prove more efficient than investing in CDR, for example.
For the record, I'm not trying to state that you're wrong in saying that buying Shoes of Focus is mathematically better (in fact, I have no idea whether you are or not), I'm just curious to learn how you reached that conclusion based on the stats alone.
2) While you are right to point out that there's some synergy between Shoes of Focus and Book of Thoth, I feel like I should mention that 3% of the 250 Mana which Shoes of Focus provides is only 7.5 Magical Power. As a result, combining Shoes of the Magi with Book of Thoth should provide 250 less Mana, but still 7.5 more Magical Power. Obviously, there's a decent chance that this synergy makes Shoes of Focus more gold-efficient than Shoes of the Magi overall if it wasn't already (since the gap in Magical Power between the two still becomes smaller with Book of Thoth involved than without it), but I just figured it's worth pointing out.
Also, I feel like some of your numbers are slightly off:
@Wayne, I don't think gold-stat efficiency is as relevant with these two items in particular compared to many others. Late game, Shoes of Focus have always been more gold efficient, 15% CDR is just a more valuable stat at that stage in the game. While 10 penetration isn't very valuable later on, it's an awesome power boost for a first item only costing ~1600g, which is why Shoes of the Magi is still a viable item (the power difference actually matters less than the penetration difference, that's why when they took away Shoes of the Magi's 10 penetration at the beginning of S2, it became kind of worthless).
Basically what it comes down to is how much you can get out of that item at that stage in the game. If you're going to be getting more out of Shoes of Focus, go that route. If you're getting roughly the same, get Shoes of Focus since they're better late game. If you're getting more out of Shoes of the Magi, enough to justify their lesser worth later on, go that route. As long as you can justify getting Shoes of the Magi, you can pick them up, the recent change to their mana just makes them harder to justify comparatively.
I talked about that because he called them "mathematically better", I realise that math in many cases is far from the most efficient way to answer a question like this properly.
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