252: Treecko S
253: Its scale wings are extremely strong and sharp. They are strong weapons that rip apart iron plates. They roam in groups of about 10. // same species name as final Sceptile. Some raptor influences here as well, evidently. Veeeeery slight resemblance to Sceptile Ruby, potentially just by coincidence
255: Torchic S
257: Every few years, its whole body is engulfed in flames and it regrows its wings. A strong-willed Pokemon that never gives up no matter how many times it loses. // [anime theme plays in background]
258: Mudkip S
277: A Pokemon with a relaxed nature. However, when it gets angry, it blows 1000 C magma out of the hump on its back. // 1200 for Numel in final lol
278: Pelipper S
282: When its body is wet by rain, it can be seen rubbing its body with leaves to polish itself. It seems that it becomes satisfied when it has a black sheen. // "Black Rock Pokemon"
283: Azurill S
284: Its body is usually cold, but gets warmer when it changes color. The zig-zag on its stomach is the only thing that doesn't change. // Kecleon
285: Wailmer S
286: Very similar to final Lombre Sapphire bar addition of "very" in final // "Mischief Pokemon"
288: Surskit S
290: Both of its eyes shine like gems. It is feared because it is said that people drawn to that beauty have their soul stolen. // Resembles final Sableye Ruby. Interestingly, it does not explicitly say that its eyes literally are gems.
291: Sharpedo S
292: Claydol S
294: A fleet-footed Pokemon that can run 50 meters in 7 seconds. It sometimes drops its children, though. It brushes its teeth by chewing on hard objects. // "Child Carry Pokemon"; see above
296: When it gets mad, it shakes its body and scatters poison spores from its head. A strong poison that could make even a pro wrestler bedridden for three days. // Similar to Shroomish Sapphire. Ah yes, measuring strength of poison in pro wrestlers, just like the measuring of electricity strength in Indian elephants
297: It is said that if you give its head petals to someone you love one-sidedly, your love will be granted. If you try to take its petals, it gets violently angry. // "Tokonatsu Pokemon"; "Everlasting Summer Pokemon" or "June / July Pokemon" depending on how you want to interpret. As R_N suggested below, concept likely evolved into Luvdisc.
298: Drinks 100L in a day. If the water it has stored in its body gets low, its the leaves on both of its hands wither. // "Shrub Pokemon". Specifically noted to have 2 hands here, if you want more imagination-inspiring deep lore about a sprinkler Pokemon. Concept is a kanji pun incorporating 灌 (in 灌水, to spray / sprinkle water, especially onto plants, and also contained in the word 灌木 (shrub) that makes up its category name).
299: It swings its head from left to right to make a beautiful xylophone-like tone. It communicates with its comrades by [alternating] this tone's scale. // As mentioned above, strongly resembles Kricketot but also has elements of the Whismur line.
305: Appears in places struck by lightning. Its horns fall off and regrow once a year and it seems that the bigger they are, the more it is respected by its peers. // "Imp Pokemon". Resembles part of final Manectric Emerald, perhaps by coincidence.
306: Often found in moist, shady areas. It blooms pretty, yellow flowers, but they have a trash-like stench. // "Peat Moss Pokemon"
307: It loves to clean off its own body as well as other Pokemon with its cotton-like wings. If its wings get dirty, it washes them in water. // resembles Swablu Sapphire
312: Wynaut S
313: Duskull S
314: Its large jaw has the power to break even boulders. An extremely stubborn Pokemon that doesn't release anything it bites. // GIVE TRAPINCH JAW LOCK
317: Each individual has flowers with different colors, so there are a lot of people that seek out rare colors. Often seen in the vicinity of pristine ponds. // Roselia
318: It drifts with the wind. In windy conditions, it wraps its tail around tree branches and waits until the wind calms down. // Similar to final Chimecho Sapphire
319: Using its sharp claws, it scratches tree roots and extracts nutrients and moisture. It uses its feelers to get a sense of its surroundings. // Identical first sentence to Nincada Sapphire
321: When it walks on land, it very quickly starts to roll. On hills, it has trouble stopping once it gets rolling. A Pokemon that is fond of people. // Spheal
322: Very similar to final Swalot Sapphire // "
Drawstring Bag Pokemon"
323: It flaps the leaves on its back to fly through the skies. A Body Slam from its hefty body can flatten even a sturdy truck in one shot. // resembles second half of final Tropius Sapphire
325: It has the power to read people's hearts. Raised by cheery people, it grows fast and blooms pretty flowers. // "heart" could be "mind" or "soul". "Flower Pokemon". Anon on 4chan noticed that it resembles pieces of both final Ralts entries
327: Huntail S
330: Its chubby body is a chunk of muscle. Said to be the strongest among Pokemon, it can carry a 10-ton truck with ease. // similar to final Hariyama Sapphire
331: Lives in small ponds overrun with aquatic plants. When its comrades assemble, they get up on waterfronts and play upbeat music. // "[Musical] Scale Pokemon". Perhaps also had some relation to Ludicolo, given reference to ponds and upbeat music.
334: It has a calm nature and dislikes conflict. It has cells in its horns that work like magnets, allowing it to take the role of a compass. // "Sightseeing Pokemon"
335: Lives in holes in trees. It capricious and struggles to bond with humans, but it has a cute face, so it's very popular as a pet. // Similar to Skitty Sapphire
336: A glutton that doesn't stop eating once it starts. It is lacks sensitivity to the point that it does not notice if it's hit, but it can't tolerate even a second of hunger. // takes parts of Numel Ruby
342: Ninjask S // "Ninja Pokemon" here rather than "Shinobi Pokemon" in final
343: Its body feels absolutely no pain. The halo above its head is thought to be the true form of this mysterious Pokemon. // Shedinja
344: Lotad S
345: It is thought that two Tapple with exactly the same spot patterns do not exist. Its shaky stride resembles dance. // "Tapple"; "Tangled Feet Pokemon". Very close to Spinda Ruby. See zpokea for more comments
346: Lunatone S // (note lack of Solrock)
347: Covered in steel armor from head to tail, it can counter any attack. // Lairon
350: Its mode of life is largely unclear. It does not have a visible mouth or ears; the only thing about it that is known is that it responds to light and sound. // "Lottery Pokemon"
359: Absol S
362: Its whole body is covered in white scales. When it flies, the scales fall off, making a sparkling belt of light in the sky. // "White Dragon Pokemon". Seems to be Taikuun.
368: First sentence of Poochyena Sapphire + Its legs are short, so it can't run very quickly.
369: It is kind and dislikes conflict, but once it gets angry, it releases great power. Always traveling with Latios. // Latias
370: A calm Pokemon, it listens obediently to people it trusts. It flies through the skies faster than a jet plane. // Resembles Latios Sapphire
372: Zigzagoon S
374: Its scale wings are extremely strong and sharp. They are strong weapons that rip apart iron plates. They roam in groups of about 10. // Copypaste of 253. "Archaeopteryx Pokemon"
382: It can extract oxygen from water, so there are cases of them living underwater. Loves eating the microorganisms in ponds. // "Dragonfly Pokemon". Masquerain is more supported here based on the reference to Surskit-esque eating of pond microorganisms
385: It hypnotizes its opponents using its dance-like movements and its deep gaze. Only female members of this Pokemon species have been found. // "Red Spider Lily Pokemon". Again, very much reminds of either Kirlia or Gardevoir; offers explanation for their fairly explicitly feminine appearance. If the "Flower" Pokemon above (325) is Ralts, it also fits decently well - the literal flower evolves into another literal flower. I forgot to mention, but the resemblance of the dress of Kirlia and Gardevoir to red spider lilies is probably not a coincidence either.
392: When in dark areas, it uses its feelers to sense for obstacles and food. Groups of them draw patterns in the sky. // Volbeat
393: Its two feelers are extremely useful. In dark areas, it uses them to read its surroundings and can even use them to carry small things. // Illumise