It was when I played Harvest Moon Boy & Girl that I realised that the strategy one should employ when upgrading any tool in Harvest Moon varies from game to game. The best strategy in Harvest Moon DS and Harvest Moon Cute DS is the worst strategy in Boy & Girl. The reverse holds true as well.
In Harvest Moon Boy & Girl, ANY tool upgrade takes three days to complete. This effectively means that you will be deprived of the use of that tool for three days. This being the case, upgrading your tools level by level is the worst strategy to employ as it means that, in the long journey from Basic level to Mystrile level, you will be deprived of each tool for a total of 12 days! That is a significant amount of time. Furthermore, the price for an upgrade remains the same, no matter how you choose to order it. In other words, it is the LEVEL of the final upgrade that determines the cost, not the number of levels that are contained in the upgrade.
Thus, upgrading a basic tool to mystrile level costs the same as upgrading a Gold Tool to Mystrile. Whenever Saibara makes a Mystrile Tool, it costs 5000G, whether he starts with a basic or a gold tool.
The best strategy in Harvest Moon Boy & Girl where tool upgrades are concerned, therefore, would be to upgrade to the highest level possible in a single order, depriving yourself of the tool only once for a period of three days. When you choose to upgrade each tool will depend on the usefulness of the tool at any given time. Obviously, the best time to upgrade a Watering Can to mystrile would be the Winter season when you have no need for it. On the other hand, you will find that a Mystrile Watering Can will be very useful throughout the growing seasons. You probably should give the tool to Saibara to upgrade to mystrile level as close to the end of the first Spring as possible, making certain that Harvest Sprites have been hired to do the watering. When your Spring crops have yielded their last harvest, there is no point in watering them further in any case.
To use the same strategy in Harvest Moon DS and Cute DS would be a mistake. In these games, the length of time needed to complete any upgrade depends on the number of levels by which the tool is upgraded. If you order an upgrade to the next level only, the job will take no more than a day. This actually means that your upgraded tool will be delivered to you the next morning at 6.00 a.m. If you made the order near the end of the previous day, you can use the tool before you order the upgrade, making any temporary deprivation totally insignificant.
There are necklaces that become available at each level of tool as well. If you skip a level or levels, you never will be able to purchase a necklace for the levels you 'missed'. Even though the cost will be greater if you order an upgrade from Grey for each level, the benefits of never being deprived of your tools far outweigh the cost factor. Money is easy to obtain in Harvest Moon DS and Cute DS, even at the start of the game, because of the treasures you can uncover in the Excavation Site. The best strategy therefore is to ask Grey to upgrade each tool by a single level only each time you order an upgrade.